Opsin evolution

Below is a large set of phylogenetically representative hand-curated opsin sequences that serves as a gene family classifier ... just blast an unknown sequence against the database below (using http://www.proweb.org/proweb/Tools/WU-blast.html) and look for consistent labelling of the top hits.

The set of sequences is not intended to be exhaustive. Rather, if a given clade has many available similar sequences, those with genome assemblies are chosen to represent the group, for example anole is preferred to ruin lizard. If the clade reflects a very deep divergence such as lamprey or amphioxus, all available sequences are provided so as to break up long branches. About half the sequences are not available from GenBank but rather are culled from trace archives, genomic contigs, and genome assemblies, typically by tblastx against the full (and growing) set of reference sequences. The level of error is low, declines with time as anomalies are noted and fixed, but never reaches zero because of problems inherent to experimental data and sequence manipulation.

Please do not add or edit sequences at this time -- email me with suggestions. tom @ cyber-dyne. com

The fasta header of each sequence is a miniature database, with fields showing the opsin type, genus, species and common name, accession number or other source, indels, introns, sequence length, lambda max adsorption, and G protein type with which it interacts. These new standardized fasta headers also serve to summarize the collection.

The protein sequences are broken into their constituent exons using genomic information when available. When not available (eg the opsin originated as a cDNA in a species lacking a genome project), the exons are inferred from the phylogenetically closest opsins. The numbers flanking exons, 012, show the phasing of each intron, eg 12 means an overhang of 1 bp at the 3' end of an exon with that fragmentary codon completed by a 2 bp overhang at the beginning of the next exon. Intron position and phasing are generally conserved over great evolutionary distances -- note here lamprey eel has identical intronation of its opsin genes orthologous to human. Cone and rod opsin paralogs are intronated identically in all species with the exception of LWS opsins which have an extra early intron of phase 12. LWS must have acquired this prior to divergence of lamprey.

Syntentic relationships are also shown. The nearest flanking HUGO-named genes are first chosen for the human opsin, two on each side. The strand orientation noted relative to a fixed convention of plus strand for the human opsin. Then each assembly is revisited to determine the extent of conservation of these flanking genes. In the event humans lack the gene, synteny is defined by the nearest diverging species, typically platypus, that has the gene. Sometimes the original synteny is only partly retained (left- or right-synteny). For deeply diverging species such as amphioxus with an assembly, flanking genes there are pushed forward into other species to help define orthologous opsins (blast clustering can be uncertain because of the diminishing percent identity).

Melanopsins, the unexpected rhabdomeric-class Gq-coupled opsin recently found in upper deuterostomes, are readily homologically confused due to various expansions and contractions. Mammals, human through platypus, have a single melanopsin. However chicken, lizard, frog, and teleost fish experienced a multiple gene segmental duplication and the resulting melanopsins were both retained (though diverged substantially). In ray-finned fish, a processed retrogene arose that may be functional in zebrafish though lost in fugu and stickleback. After its whole genome duplication, zebrafish also retained two copies of the original melanopsin. Chondrichthyes also have a second copy of the primary melanopsin but synteny -- which is essential for analysis since intron placement is uninformative in duplications and sequence alignment is too dependent on unknown rates -- is not available in the current contig-level assembly.

Amphioxus also contains two melanopsins from an apparently independent duplication. Flanking gene order today bears no relation to vertebrate gene order. The lamprey situation awaits assembly of its traces or targeted transcript studies. At this time, only a four exon fragmentary melanopsin can be recovered (however with high percent identity, 80%). Possibly orthologs of this melanopsin locus could be tracked into the highly derived tunicates, acorn worm, and sea urchins. The distinctive intron pattern may even allow melanopsin antecedents to be identified in Cnidaria and Protostomia. At this point, the best blastp match to insects stands at 37% with no evident syntenic or intronic support

While clade-specific proliferation of melanopsins -- and implied role subfunctionalization -- confounds the situation for chordates, it really has little impact on the opsin classifier described here. Unknown sequences will readily find their place because of excellent phylogenetic distribution of reference sequences and the inherent distance of melanopsins from the ciliary collection. The main utility at the level of opsin classifier is the ability to identify other rhabdomeric opsins in later deuterostomes should they occur. At the level of alignment, the melanopsis serve as outgroup to ciliary opsins and so help define motifs specific to Gt-coupled signaling and other structure/function issues.

>RHO1_homSap	Homo	sapiens	(human)	Gt	0...2.1.0.0	-MBD4	+IFT122	+H1FOO	-PLXND1	indel	349 aa	497 nm		rod_rhodopsin	RHO
>RHO1_monDom	Monodelphis	domesticus	(opossum)	Gt	0...2.1.0.0	-MBD4	+IFT122	+H1FOO	-PLXND1	indel	349 aa	000 nm		rod_rhodopsin	
>RHO1_ornAna	Ornithorhynchus	anatinus	(platypus)	Gt	0...2.1.0.0	-	+IFT122	-	-PLXND1	indel	354 aa	000 nm		rod_rhodopsin	
>RHO1_galGal	Gallus	gallus	(chicken)	Gt	0...2.1.0.0	-MBD4	+IFT122	+H1FOO	-PLXND1	indel	352 aa	000 nm		rod_rhodopsin	RH1
>RHO1_anoCar	Anolis	carolinensis	(lizard)	Gt	0...2.1.0.0	-MBD4	+IFT122	-	-PLXND1	indel	343 aa	000 nm		rod_rhodopsin	
>RHO1_xenTro	Xenopus	tropicalis	(frog)	Gt	0...2.1.0.0	-MBD4	+IFT122	-	-PLXND1	indel	355 aa	000 nm		rod_rhodopsin	
>RHO1_neoFor	Neoceratodus	forsteri	(lungfish)	Gt	0...2.1.0.0	x	x	x	x	indel	355 aa	000 nm	17961206	rod_rhodopsin	
>RHO1_latCha	Latimeria	chalumnae	(coelacanth)	Gt	0...2.1.0.0	x	x	x	x	indel	355 aa	478 nm	10339578	rod_rhodopsin	
>RHO1_takRub	Takifugu	rubripes	(pufferfish)	Gt	0...2.1.0.0	-MBD4	+IFT122	-	-PLXND1	indel		000 nm		rod_rhodopsin	
>RHO1_leuEri	Leucoraja	erinacea	(skate)	Gt	0...2.1.0.0	x	x	x	x	indel	355 aa	000 nm		rod_rhodopsin	
>RHO1_calMil	Callorhinchus	milii	(elephantfish)	Gt	0...2.1.0.0	x	x	x	x	indel	355 aa	000 nm		rod_rhodopsin	
>RHO1_petMar	Petromyzon	marinus	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	354 aa	000 nm		rod_rhodopsin	
>RHO1_geoAus	Geotria	australis	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	354 aa	497 nm	17463225	rod_rhodopsin	
>RHO1_letJap	Lethenteron	japonicum	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	354 aa	000 nm		cone_rhodopsin	
>RHO2_galGal	Gallus	gallus	(chicken)	Gt	0...2.1.0.0	-IHPK3	-LEMD2	-GRM4	+HMGA1	indel	356 aa	000 nm		cone_rhodopsin	
>RHO2_anoCar	Anolis	carolinensis	(lizard)	Gt	0...2.1.0.0	-IHPK3	-LEMD2	-GRM4	+HMGA1	indel	356 aa	000 nm		cone_rhodopsin	
>RHO2_gekGek	Gekko	gekko	(gecko)	Gt	0...2.1.0.0	x	x	x	x	indel	356 aa	000 nm		cone_rhodopsin	
>RHO2_neoFor	Neoceratodus	forsteri	(lungfish)	Gt	0...2.1.0.0	x	x	x	x	indel	356 aa	000 nm	17961206	cone_rhodopsin	
>RHO2_latCha	Latimeria	chalumnae	(coelacanth)	Gt	0...2.1.0.0	x	x	x	x	indel	355 aa	485 nm	10339578	cone_rhodopsin	RH2
>RHO2_geoAus	Geotria	australis	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	355 aa	492 nm	17463225	cone_rhodopsin	RhB
>SWS2_ornAna	Ornithorhynchus	anatinus	(platypus)	Gt	0...2.1.0.0	-IRAK1	-MECP2	-	+TKTL1	indel	364 aa	000 nm		cone_short2	
>SWS2_galGal	Gallus	gallus	(chicken)	Gt	0...2.1.0.0	x	x	x	x	indel	362 aa	000 nm		cone_short2	
>SWS2_taeGut	Taeniopygia	guttata	(finch)	Gt	0...2.1.0.0	x	x	x	x	indel	363 aa	000 nm		cone_short2	
>SWS2_utaSta	Uta	stansburiana	(lizard)	Gt	0...2.1.0.0	x	x	x	x	indel	364 aa	000 nm		cone_short2	
>SWS2_xenTro	Xenopus	tropicalis	(frog)	Gt	0...2.1.0.0	-IRAK1	-MECP2	-	-	indel	363 aa	000 nm		cone_short2	
>SWS2_neoFor	Neoceratodus	forsteri	(lungfish)	Gt	0...2.1.0.0	x	x	x	x	indel	364 aa	000 nm	17961206	cone_short2	
>SWS2_takRub	Takifugu	rubripes	(pufferfish)	Gt	0...2.1.0.0	x	x	x	x	indel	351 aa	000 nm	genome	cone_short2	
>SWS2_gasAcu	Gasterosteus	aculeatus	(stickleback)	Gt	0.2.2.1.0.0	x	x	x	x	indel	359 aa	000 nm	genome	cone_short2	
>SWS2_geoAus	Geotria	australis	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	362 aa	439 nm	17463225	cone_short2	
>SWS1_homSap	Homo	sapiens	(human)	Gt	0.2.2.1.0.0	-FAM137A	-CALU	-NAG6	-FLNC	indel	348 aa	000 nm		cone_short1	
>SWS1_monDom	Monodelphis	domesticus	(opossum)	Gt	0...2.1.0.0	-FAM137A	-CALU	-NAG6	-FLNC	indel	347 aa	000 nm		cone_short1	
>SWS1_galGal	Gallus	gallus	(chicken)	Gt	0...2.1.0.0	x	x	x	x	indel	348 aa	000 nm		cone_short1	
>SWS1_taeGut	Taeniopygia	guttata	(finch)	Gt	0...2.1.0.0	x	x	x	x	indel	347 aa	000 nm		cone_short1	
>SWS1_anoCar	Anolis	carolinensis	(lizard)	Gt	0.2.2.1.0.0	x	-CALU	x	x	indel	347 aa	000 nm	genome	cone_short1	
>SWS1_utaSta	Uta	stansburiana	(lizard)	Gt	0...2.1.0.0	x	x	x	x	indel	348 aa	000 nm		cone_short1	
>SWS1_xenLae	Xenopus	laevis	(frog)	Gt	0...2.1.0.0	-	-CALU	-	-	indel	348 aa	000 nm		cone_short1	
>SWS1_neoFor	Neoceratodus	forsteri	(lungfish)	Gt	0...2.1.0.0	x	x	x	x	indel	347 aa	000 nm	17961206	cone_short1	
>SWS1_danRer	Danio	rerio	(zebrafish)	Gt	0...2.1.0.0	-	-CALU	-	-	indel	337 aa	000 nm		cone_short1	
>SWS1_oryLat	Oryzias	latipes	(medaka)	Gt	0...2.1.0.0	-	-	-	-	indel	336 aa	000 nm		cone_short1	
>SWS1_geoAus	Geotria	australis	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	346 aa	359 nm	17463225	cone_short1	
>LWS_homSap	Homo	sapiens	(human)	Gt	0.2.2.1.0.0	-IRAK1	-MECP2	-TEX28	+TKTL1	indel	364 aa	530 nm		cone_long	OPN1MW
>LWS_monDom	Monodelphis	domesticus	(opossum)	Gt	0.2.2.1.0.0	-IRAK1	-MECP2	-	+TKTL1	indel	368 aa	000 nm		cone_long	
>LWS_ornAna	Ornithorhynchus	anatinus	(platypus)	Gt	0.2.2.1.0.0	-IRAK1	-MECP2	-	-	indel	365 aa	000 nm		cone_long	
>LWS_galGal	Gallus	gallus	(chicken)	Gt	0.2.2.1.0.0	x	x	x	x	indel	363 aa	000 nm		cone_long	
>LWS_anoCar	Anolis	carolinensis	(lizard)	Gt	0.2.2.1.0.0	-	-	-TEX28	+TKTL1	indel	370 aa	000 nm		cone_long	
>LWS_xenTro	Xenopus	tropicalis	(frog)	Gt	0.2.2.1.0.0	-IRAK1	-MECP2	-	-	indel		000 nm		cone_long	
>LWS_neoFor	Neoceratodus	forsteri	(lungfish)	Gt	0.2.2.1.0.0	x	x	x	x	indel	365 aa	000 nm	17961206	cone_long	
>LWS_takRub	Takifugu	rubripes	(pufferfish)	Gt	0...2.1.0.0	x	x	x	x	indel	358 aa	000 nm	genome		
>LWS_gasAcu	Gasterosteus	aculeatus	(stickleback)	Gt	0.2.2.1.0.0	-	-	-	-	indel	358 aa	000 nm	genome	cone_long	
>LWS_petMar	Petromyzon	maritimus	(lamprey)	Gt	0.2.2.1.0.0	x	x	x	x	indel	366 aa	000 nm		cone_long	
>LWS_letJap	Lethenteron	japonicum	(lamprey)	Gt	0.2.2.1.0.0	x	x	x	x	indel	365 aa	000 nm		cone_long	
>LWS_geoAus	Geotria	australis	(lamprey)	Gt	0.2.2.1.0.0	x	x	x	x	indel	365 aa	560 nm	17463225	cone_long	
>PIN_galGal	Gallus	gallus	(chicken)	Gt	0...2.2.0.0					indel	352 aa	000 nm		pinopsin	
>PIN_utaSta	Uta	stansburiana	(lizard)	Gt	0...2.2.0.0	x	x	x	x	indel	359 aa	000 nm		pinopsin	
>PIN_pheMad	Phelsuma	madagascariensis	(gecko)	Gt	0...2.2.0.0	x	x	x	x	indel	358 aa	000 nm		pinopsin	
>PIN_podSic	Podarcis	sicula	(lizard)	Gt	0...2.2.0.0	x	x	x	x	indel	354 aa	000 nm		pinopsin	
>PIN_xenTro	Xenopus	tropicalis	(frog)	Gt	0...2.2.0.0					indel	346 aa	000 nm		pinopsin	
>PIN_bufJap	Bufo	japonicus	(frog)	Gt	0...2.2.0.0	x	x	x	x	indel	347 aa	000 nm		pinopsin	
>VAOP_galGal	Gallus	gallus	(chicken)	Gt	0...2.1.0.0	+INPP5A	-NXK6	+C10orf61	+ALDH18A1	indel	393 aa	000 nm		vertebrate_ancient	
>VAOP_anoCar	Anolis	carolinensis	(lizard)	Gt	0...2.1.0.0	+INPP5A	-NXK6	+GPR125	+KNDC1	indel	389 aa	000 nm		vertebrate_ancient	
>VAOP_xenTro	Xenopus	tropicalis	(frog)	Gt	0...2.1.0.0	-	+GSTO2	-C10orf92	-	indel	383 aa	000 nm		vertebrate_ancient	
>VAOP_danRer	Danio	rerio	(zebrafish)	Gt	0...2.1.0.0	-	-	-	-	indel	378 aa	000 nm		vertebrate_ancient	
>VAOP_takRub	Takifugu	rubripes	(teleost)	Gt	0...2.1.0.0	+INPP5A	-NXK6	-	+KNDC1	indel	362 aa	000 nm		vertebrate_ancient	
>VAOP_rutRut	Rutilus	rutilus	(minnow)	Gt	0...2.1.0.0	x	x	x	x	indel	383 aa	000 nm		vertebrate_ancient	
>VAOP_petMar	Petromyzon	marinus	(lamprey)	Gt	0...2.1.0.0	x	x	x	x	indel	445 aa	000 nm	9427550	vertebrate_ancient	
>PPIN_anoCar	Anolis	carolinensis	(lizard)	Gt	0...2...0.0	-CPEB2	-CACNA2D3	+SELK	+ACTR8	indel	346 aa	000 nm		parapinopsin	
>PPIN_xenTro	Xenopus	tropicalis	(frog)	Gt	0...2...0.0	-	-	+SELK	-	indel	349 aa	000 nm		parapinopsin	
>PPIN_ictPun	Ictalurus	punctatus	(catfish)	Gt	0...2...0.0	x	x	x	x	indel	347 aa	000 nm		parapinopsin	
>PPIN_danRer	Danio	rerio	(zebrafish)	Gt	0...2...0.0	-	-	+SELK	-	indel	338 aa	000 nm		parapinopsin	
>PPIN_oncMyk	Oncorhynchus	mykiss	(trout)	Gt	0...2...0.0	x	x	x	x	indel	347 aa	000 nm		parapinopsin	
>PPIN_petMar	Petromyzon	maritimus	(lamprey)	Gt	0...2...0.0	x	x	x	x	indel	344 aa	000 nm		parapinopsin	
>PPIN_letJap	Lethenteron	japonicum	lamprey	Gt	0...2...0.0	x	x	x	x	indel	344 aa	000 nm		parapinopsin	
>PPINa_cioInt	Ciona	intestinalis	(tunicate)	Gt	0...2...0.0	-HOXB1	+HHEX	+CUL4A	-	indel	391 aa	000 nm	11591373	parapinopsin	
>PPINb_cioInt	Ciona	intestinalis	(tunicate)	Gt	0...2...0.0	-TMEM165	+FUT4	-	-	indel	353 aa	000 nm		parapinopsin	
>PARIE_utaSta	Uta	stansburiana	(lizard)	Gd+Go	0...2...0.0	x	x	x	x	indel	347 aa	522 nm	16543463	parietopsin	
>PARIE_anoCar	Anolis	carolinensis	(lizard)	Gd+Go	0...2...0.0	+EEA1	-FLJ46688	+BTG1	-	indel	347 aa	000 nm	16543463	parietopsin	
>PARIE_xenTro	Xenopus	tropicalis	(frog)	Gd+Go	0...2...0.0	-lum	-DCN	-	-	indel	346 aa	000 nm	16543463	parietopsin	
>PARIE_takRub	Takifugu	rubripes	(teleost)	Gd+Go	0...2...0.0	-HSP90B1	+NT5DC2	-KCND3	-FLNC	indel	 351 aa	000 nm	16543463	parietopsin	
>PARIE_gasAcu	Gasterosteus	aculeatus	(stickleback)	Gd+Go	0...2...0.0	-HSP90B1	+NT5DC2	-KCND3	-FLNC	indel	361 aa	000 nm	-	parietopsin	
>PARIE_danRer	Danio	rerio	(zebrafish)	Gd+Go	0...2...0.0	-	+NT5DC2	+FBXL13	-	indel	337 aa	000 nm	16543463	parietopsin	
>ENCEPH_homSap	Homo	sapiens	(human)	Gt	0...2...0.0	-EXO1	-WDR64	-KMO	+FH	indel	403 aa	000 nm		parietopsin	OPN3
>ENCEPH_monDom	Monodelphis	domestica	(opossum)	Gt	0...2...0.0	-EXO1	-WDR64	-KMO	+FH	indel	411 aa	000 nm		encephalopsin	OPN3
>ENCEPH_galGal	Gallus	gallus	(chicken)	Gt	0...2...0.0	-EXO1	-WDR64	-PIGM	+RGS7	indel	396 aa	000 nm		encephalopsin	OPN3
>ENCEPH_anoCar	Anolis	carolinensis	(lizard)	Gt	0...2...0.0	-EXO1	-WDR64	-PIGM	+RGS7	indel	408 aa	000 nm		encephalopsin	OPN3
>ENCEPH_xenTro	Xenopus	tropicalis	(frog)	Gt	0...2...0.0	-ASAH3L	+RPS6	-ADFP	-DENND4C	indel	401 aa	000 nm		encephalopsin	OPN3
>ENCEPH4a_takRub	Takifugu	rubripes	(teleost)	Gt	0...2...0.0	-CALD1	+TNK2	-RAB18	+ABI1	indel	403 aa	000 nm		encephalopsin	TMT
>ENCEPH4b_takRub	Takifugu	rubripes	(teleost)	Gt	0...2...0.0					indel	407 aa	000 nm		encephalopsin	OPN3
>ENCEPH_takRub	Takifugu	rubripes	(teleost)	Gt	0...2...0.0	-	+PTK7	-KMO	+IDE	indel		000 nm			
>ENCEPH_tetNig	Tetraodon	nigroviridis	(pufferfish)	Gt	0...2...0.0	-	-	-	-	indel	388 aa	000 nm		encephalopsin	OPN3
>ENCEPH_gasAcu	Gasterosteus	aculeatus	(stickleback)	Gt	0...2...0.0		+CDC42EP3	-KMO	+IDE	indel	389 aa	000 nm		encephalopsin	OPN3
>ENCEPH4_braFlo	Branchiostoma	floridae	(amphioxus)	Gt						indel	402 aa	000 nm		encephalopsin	Amphiop4
>ENCEPH4_braBel	Branchiostoma	belcheri	(amphioxus)	Gt		x	x	x	x	indel	401 aa	000 nm		encephalopsin	Amphiop4
>ENCEPH5_braBel	Branchiostoma	belcheri	(amphioxus)	Gt		x	x	x	x	indel	421 aa	000 nm		encephalopsin	Amphiop5
>ENCEPH5_braFlo	Branchiostoma	floridae	(amphioxus)	Gt						indel	409 aa	000 nm		encephalopsin	
>ENCEPH_apiMel	Apis	mellifera	(bee)	Gt						indel	329 aa	000 nm		encephalopsin	
>ENCEPH1_anoGam	Anopheles	gambiae	(mosquito)	Gt						indel	461 aa	000 nm		encephalopsin	
>ENCEPH2_anoGam	Anopheles	gambiae	(mosquito)	Gt						indel	434 aa	000 nm		encephalopsin	
>CILL2_plaDum	Platynereis	dumerilii	(ragworm)	Gt		x	x	x	x	indel	310 aa	000 nm		proto_cilliary	
>CILL1_plaDum	Platynereis	dumerilii	(ragworm)	Gt		x	x	x	x	indel	355 aa	000 nm		proto_cilliary	
>RGR_homSap	Homo	sapiens	(human)	??		PCDH21	LRRC21	GRID1	WAPAL	indel	296 aa	000 nm		retinal_ganglia	RGR
>PER_homSap	Homo	sapiens	(human)	??		CFI	NOLA1	EGF	ELOVL6	indel	338 aa	000 nm		peropsin	RRH
>PERa_braBel	Branchiostoma	belcheri	(amphioxus)	??		x	x	x	x	indel	365 aa	000 nm		peropsin	Amphiop3
>PERb_braBel	Branchiostoma	belcheri	(amphioxus)	??		x	x	x	x	indel	522 aa	000 nm		peropsin	Amphiop2
>PERc_braBel	Branchiostoma	belcheri	(amphioxus)	Go		x	x	x	x	indel	391 aa	000 nm		peropsin	Amphiop1
>NEUR_homSap	Homo	sapiens	(human)	??		+CD2AP	+GPR115	-C6orf138	-MUT	indel	355 aa	000 nm		neuropsin	OPN5
>MEL1_homSap	Homo	sapiens	(human)	Gq		-GRID1	-WAPAL	+LDB3	+BMPR1A	indel	479 aa	000 nm		melanopsin	OPN4
>MEL1_monDom	Monodelphis	domestica	(opossum)	Gq		-GRID1	-WAPAL	+LDB3	+BMPR1A	indel		000 nm		melanopsin	OPN4
>MEL1_galGal	Gallus	gallus	(chicken)	Gq		-GRID1	-WAPAL	+LDB3	+BMPR1A	indel		000 nm	16856781	melanopsin	OPN4m
>MEL1_xenTro	Xenopus	tropicalis	(frog)	Gq		-GRID1	-WAPAL	+LDB3	+BMPR1A	indel	596 aa	000 nm	16856781	melanopsin	OPN4m
>MEL1_danRer	Danio	rerio	(zebrafish)	Gq		-	+USP54	+LDB3	+BMPR1A	indel		000 nm		melanopsin	OPN4m
>MEL1D_danRer	Danio	rerio	(zebrafish)	Gq		-	+USP54	+LDB3	+BMPR1A	indel		000 nm			
>MEL1_takRub	Takifugu	rubripes	(teleost)	Gq		-	+USP54	+LDB3	+BMPR1A	indel		000 nm		melanopsin	OPN4m
>MEL1_gasAcu	Gasterosteus	aculeatus	(stickleback)	Gq		-	-	+LDB3	+BMPR1A	indel		000 nm		melanopsin	OPN4m
>MEL1_oryLat	Oryzias	latipes	(medaka)	Gq		-	+USP54	+LDB3	+BMPR1A	indel		000 nm		melanopsin	OPN4m
>MEL1_calMil	Callorhinchus	milii	(elephantfish)	Gq		-	-	-	-	indel		000 nm		melanopsin	OPN4m
>MEL1a_braFlo	Branchiostoma	floridae	(amphioxus)	Gq		-	-	-	-	indel	709 aa	000 nm		melanopsin	Amphi-mop
>MEL1a_braBel	Branchiostoma	belcheri	(amphioxus)	Gq		x	x	x	x	indel	707 aa	000 nm		melanopsin	Amphi-mop
>MEL1b_braFlo	Branchiostoma	floridae	(amphioxus)	Gq		-	-	-	-	indel		000 nm			
>MEL1b_braBel	Branchiostoma	belcheri	(amphioxus)	Gq		x	x	x	x	indel	402 aa	000 nm		melanopsin	Amphiop6
>MEL2_galGal	Gallus	gallus	(chicken)	Gq		+GRID2+SMARCAD1	-PGDS	-SEC24B	+COL25A1	indel	544 aa	000 nm	17977531	melanopsin	
>MEL2_anoCar	Anolis	carolinensis	(lizard)	Gq		+GRID2+SMARCAD1	-ATOH1	+PDLIM5	+BMPR1B	indel	290 aa	000 nm		melanopsin	
>MEL2_xenLae	Xenopus	laevis	(frog)	Gq		+SMARCAD1		+PDLIM5	+BMPR1B	indel	535 aa	000 nm		melanopsin	Xmop
>MEL2_danRer	Danio	rerio	(zebrafish)	Gq		-	+FLJ39155	+PDLIM5	-	indel		000 nm			
>MEL2_tetNig	Tetraodon	nigroviridis	(pufferfish)	Gq		-	-	-	+BMPR1B	indel	404 aa	000 nm		melanopsin	
>MEL2_gasAcu	Gasterosteus	aculeatus	(stickleback)	Gq		KNTC2	+FLJ39155	+PDLIM5	+BMPR1B	indel	353 aa	000 nm		melanopsin	
>RHAB_plaDum	Platynereis	dumerilii	(polychaete)	Gq		x	x	x	x	indel	383 aa	000 nm		rhabdomeric	
>RHAB1_apiMel	Apis	mellifera	(bee)	Gq						indel	378 aa	000 nm		rhabdomeric	Lop1
>RHAB2_apiMel	Apis	mellifera	(bee)	Gq						indel	386 aa	000 nm		rhabdomeric	Lop2
>RHAB3_apiMel	Apis	mellifera	(bee)	Gq						indel	372 aa	000 nm		rhabdomeric	
>RHAB4_apiMel	Apis	mellifera	(bee)	Gq						indel	378 aa	000 nm		rhabdomeric	Blop

>RHO1_homSap rhodopsin ciliary all GT-AG chr3:130,730,172 3q22.1 + 6706 5 12 21 00 00
0 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG 1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 2
1 YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 0
0 FRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA* 0

>RHO1_monDom Monodelphis opossum 349
0 MNGTEGPNFYVPFSNKTGTVRSPFEEPQYYLADPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTMTLYTSLHGYFVFGPTGCNLEGFFATLG 1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIIGVAFTWVMALACAFPPLIGWSR 2
1 YIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTIPAFFAKSSSVYNPVIYIMMNKQ 0
0 FRTCMITTLCCGKNPLGDDEASATASKTETSQVAPA* 0

>RHO1_ornAna rhodopsin rod pigment Ultra20:114,479-118,391
0 MNGTEGQDFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSVLAAYMFMLIMLGFPINFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVLGGFTTTLYTSLHGYFVFGPTGCNIEGFFATLG 1
2 GEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACALPPLVGWSR 2
1 YIPEGMQCSCGIDYYTLRPEVNNESFVIYMFVVHFTIPMTIIFFCYGRLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTVPAFFAKSSAIYNPVIYIMMNKQ 0
0 FRNCMLTTICCGKNPLGDDEASATASKTEQSSVSTSQVSPA* 0

>RHO1_galGal RH1 RDP1 rhodopsin rod galGal+ ornAna+ homSap+
0 MNGTEGQDFYVPMSNKTGVVRSPFEYPQYYLAEPWKFSALAAYMFMLILLGFPVNFLTLYVTIQHKKLRTPLNYILLNLVVADLFMVFGGFTTTMYTSMNGYFVFGVTGCYIEGFFATLG 1
2 GEIALWSLVVLAVERYVVVCKPMSNFRFGENHAIMGVAFSWIMAMACAAPPLFGWSR 2
1 YIPEGMQCSCGIDYYTLKPEINNESFVIYMFVVHFMIPLAVIFFCYGNLVCTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTNQGSDFGPIFMTIPAFFAKSSAIYNPVIYIVMNKQ 0
0 FRNCMITTLCCGKNPLGDEDTSAGKTETSSVSTSQVSPA* 0

>RHO1_anoCar Anolis lizard
0 MNGTEGQNFYVPMSNKTGVVRNPFEYPQYYLADPWQFSALAAYMFLLILLGFPINFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVLMGFTTTMYTSMNGYFIFGTVGR 2
2 GEMGLWSLVVLAVERYVVICKPMSNFRFGETHALIGVSCTWIMALACAGPPLLGWSR 2
1 YIPEGMQCSCGVDYYTPTPEVHNESFVIYMFLVHFVTPLTIIFFCYGRLVCTVKA 0
0 AAAQQQESATTQKAEREVTRMVVIMVISFLVCWVPYASVAFYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQ 0
0 FRNCMIMTLCCGKNPLGDEDTSAGTKTETSTVSTSQVSPA* 0

>RHO1_xenTro frog 354
0 MNGTEGPNFYIPMSNKTGVVRSPFDYPQYYLAEPWKYSALAAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMHGYFIFGQTGCYIEGFFATLG 1
2 GEMALWSLVVLAIERYVVVCKPMANFRFGENHAIMGVVFTWIMALSCAAPPLFGWSR 2
1 YIPEGMQCSCGVDYYTLKPEVNNESFVVYMFIVHFTIPLCVIFFCYGRLLCTVKE 0
0 AAAQQQESATTQKAEKEVTRMVVMMVIFFLICWVPYAYVAFYIFTHQGSDFGPVFMTVPAFFAKSSAIYNPVIYIVLNKQ 0
0 FRNCLITTLCCGKNPFGDEEGSSAASSKTEASSVSSSQVSPA* 0

>RHO1_neoFor Neoceratodus forsteri (Australian lungfish)
0 MNGTEGPNFYVPMTNKTGVVRSPFEYPQYYLADPWKYSALAAYMFFLILTGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTAMNGYFVFGVVGCNLEGFFATFG 1
2 GIIALWCLVVLAIERYIVVCKPISNFRFGENHAIMGVVFTWIMALACAGPPLFGWSR 2
1 YIPEGMQCSCGIDYYTLKPEVNNESFVIYMFIVHFTIPLIIIFFCYGRLMCTVKE 0
0 AAAQQQESATTQKAEKEVTRMVYIMVISYLVCWLPYASVSFYIFTHQGSDFGPVFMTVPAFFAKTASVYNPVIYILMNKQ 0
0 FRNCMITTLCCGKNPFGDEETTSAGTSKTEASSVSSSQVSPA* 0

>RHO1_latCha Latimeria chalumnae (coelacanth)
0 MNGTEGPNFYVPMSNKTGVVRNPFEYPQYYLADPWKYSALAAYMFFLILVGFPINFLTLFVTIQHKKLRTPLNYILLDLAVADLCMVFGGFFVTMYSSMNGYFVLGPTGCNIEGFFATLG 1
2 GQVALWALVVLAIERYVVVCKPMSNFRFGENHAIMGVIFTWIMALSCAVPPLFGWSR 2
1 YIPEGMQSSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGRLVCTVKD 0
0 AAAQQQESATTQKAEKEVTRMVIVMVISFLVCWVPYASVAAYIFFNQGSEFGPVFMTAPSFFAKSASFYNPVIYILLNKQ 0
0 FRNCMITTLCCGKNPFGDEDATSAAGSSKTEASSVSSSSVSPA* 0

>RHO1_takRub Takifugu rubripes (pufferfish)
0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWKYSLVAAYMLFLIITAFPVNFLTLFVTVKHKKLRTPLNYVLLNLAVADLFMVIGGFTVTLYTALHAYFVLGVTGCNIEGFFATLG 1
2 GEIALWSLVVLAVERYIVVCKPMTNFRFGEKHAIAGLVFTWIMALTCATPPLLGWSR 2
1 YIPEGMQCSCGIDYYTPKPEINNTSFVIYMFILHFSIPLAIIFFCYSRLLCTVRA 0
0 AAALQQESETTQRAEKEVTRMVIVMVISFLVCWVPYASVAWYIFANQGTEFGPVFMTAPAFFAKSAALYNPVIYILLNRQ 0
0 FRNCMITTVCCGKNPFGDDDAATTVSKTQSSSVSSSQVAPA* 0

>RHO1_leuEri Leucoraja erinacea rod opsin 
0 MNGTEGENFYVPMSNKTGVVRSPFDYPQYYLGEPWMFSALAAYMFFLILTGLPVNFLTLFVTIQHKKLRQPLNYILLNLAVSDLFMVFGGFTTTIITSMNGYFIFGPAGCNFEGFFATLG 1
2 GEVGLWCLVVLAIERYMVVCKPMANFRFGSQHAIIGVVFTWIMALSCAGPPLVGWSR 2
1 YIPEGLQCSCGVDYYTMKPEVNNESFVIYMFVVHFTIPLIVIFFCYGRLVCTVKE 0
0 AAAQQQESESTQRAEREVTRMVIIMVVAFLICWVPYASVAFYIFINQGCDFTPFFMTVPAFFAKSSAVYNPLIYILMNKQ 0
0 FRNCMITTICLGKNPFEEEESTSASASKTEASSVSSSQVAPA* 0

>RHO1_calMil Callorhinchus milii complete wgs
0 MNGTEGENFYIPMSNKTGVVRSPFEYPQYYLAEPWQFSILAAYMFFLIITCFPVNFLTLYVTFEHKKLRQPLNFILLNLAVADLFMVFGGFFITVYTSLHGYFVFGVTGCNFEGFFATLG 1
2 GEIGLWSLVVLAIERYVVVCKPMSNFRFGTNHAIMGVAFTWVMALACAVPPLMGWSR 2
1 YIPEGLQCSCGVDYYTLKPEINNESFVIYMFVVHFLIPLIIIFFCYGRLVCTVKE 0
0 AAAQQQESESTQRAEREVTRMVIIMVIFFLICWVPYASVAFFIFTNQGSEFGPIFMAVPAFFAKSSALYNPLIYILLNKQ 0
0 FRNCMITTLCCGKNPFEEDESTSAAASKTEASSVSSSQVSPA* 0

>RHO1_petMar lamprey Petromyzon marinus introns from U67123
0 MNGTEGENFYIPFSNKTGLARSPFEYPQYYLAEPWKYSVLAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAVANLFMVLFGFTLTMYSSMNGYFVFGPTMCNFEGFFATLG 1
2 GEMSLWSLVVLAIERYIVICKPMGNFRFGSTHAYMGVAFTWFMALSCAAPPLVGWSR 2
1 YLPEGMQCSCGPDYYTLNPNFNNESFVIYMFLVHFIIPFIVIFFCYGRLLCTVKE 0
0 AAAAQQESASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTVPAFFAKTSALYNPIIYILMNKQ 0
0 FRNCMITTLCCGKNPLGDEDSGASTSKTEVSSVSTSQVSPA* 0

>RHO1_geoAus lamprey Geotria australis rodRhA introns by homology
0 MNGTEGQNFYIPFSNKTDVARSPFEYPQYYLAEPWKFSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAVSNLFMILFGFTTTMYTSMNGYFVFGPTMCSIEGFFATLG 1
2 GEVSLWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVALTWVMALSCAAPPLLGWSR 2
1 YLPEGMQCSCGPDYYTMNPTYNNESFVIYMFIVHFTIPFVIIFFSYGRLLCTVKE 0
0 AAAAQQESASTQKAEKEVTRMVVLMVVGFLVCWVPYASVAFYIFTNQGSDFGATFMTLPAFFAKSSALYNPVIYILMNKQ 0
0 FRNCMITTLCCGKNPLGDDDSGASTSKTEVSSVSTSQVAPA* 0

>RHO1_letJap lamprey Lethenteron japonicum introns by homology
0 MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG 1
2 GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSR 2
1 YIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKE 0
0 AAAAQQESASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSALYNPVIYILMNKQ 0
0 FRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSQVSPA* 0

>RHO2_galGal rhodopsin-like cone galGal+ ornAna- homSap-
0 MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG 1
2 GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSR 2
1 YMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVRE 0
0 AAAQQQESATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSLYNPIIYVLMNKQ 0
0 FRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA* 0

>RHO2_anoCar rhodopsin-like cone anoCar+ HMGA1 GRM4 RHO2 MLN LEMD2 IHPK3
0 MNGTEGINFYVPLSNKTGLVRSPFEYPQYYLAEPWKYKVVCCYIFFLIFTGLPINILTLLVTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFIFGPIGCAIEGFFATLG 1
2 GQVALWSLVVLAIERYIVVCKPMGNFRFSATHALMGISFTWFMSFSCAAPPLLGWSR 2
1 YIPEGMQCSCGPDYYTLNPDYHNESYVLYMFGVHFVIPVVVIFFSYGRLICKVRE 0
0 AAAQQQESASTQKAEREVTRMVILMVLGFLLAWTPYAMVAFWIFTNKGVDFSATLMSVPAFFSKSSSLYNPIIYVLMNKQ 0
0 FRNCMITTICCGKNPFGDEDVSSSVSQSKTEVSSVSSSQVSPA* 0

>RHO2_gekGek Gekko gekko 467 Cone visual pigments are present in gecko rod cells
0 MNGTEGINFYVPLSNKTGLVRSPFEYPQYYLADPWKFKVLSFYMFFLIAAGMPLNGLTLFVTFQHKKLRQPLNYILVNLAAANLVTVCCGFTVTFYASWYAYFVFGPIGCAIEGFFATIG 1
2 GQVALWSLVVLAIERYIVICKPMGNFRFSATHAIMGIAFTWFMALACAGPPLFGWSR 2
1 FIPEGMQCSCGPDYYTLNPDFHNESYVIYMFIVHFTVPMVVIFFSYGRLVCKVRE 0
0 AAAQQQESATTQKAEKEVTRMVILMVLGFLLAWTPYAATAIWIFTNRGAAFSVTFMTIPAFFSKSSSIYNPIIYVLLNKQ 0
0 FRNCMVTTICCGKNPFGDEDVSSSVSQSKTEVSSVSSSQVAPA* 0

>RHO2_neoFor Neoceratodus forsteri (Australian lungfish)
0 MNGTEGINFYVPHSNKTGVVRSPFEYPQYYLADPWKYSIVCAYMFFLIITGLPINLLTLVVTFKHKKLRQPLNYILVNLAVADLFMVCFGFTVTFSTAINGYFIFGPRGCAIEGFMATLG 1
2 GEVALWSLVVLAIERYIVVCKPMGNFRFSNNHSIIGIVFTWLAALSCAAPPLFGWSR 2
1 YLPEGMQCSCGPDYYTMNPDYHNESFVIYMFVVHFFIPVIVIFVSYGRLICKVKE 0
0 AAAQQQESASTQKAEREVTRMVILMVIGFMTAWTPYATVAFWIFMNKGAEFGATFMAAPAFFSKSSALYNPIIYVLMNKQ 0
0 FRNCMVTTLCCGKNPFGDDDVSSSVSAGKTEVSSVSSSQVSPA* 0

>RHO2_latCha Latimeria chalumnae (coelacanth) RH2 opsin
0 MNGTEGMNFYVPLSNRTGLVRSPFEYTQYYLAEPWKFSVLCAYMFLLIILGFPINFLTLLVTFKHKKLRQPLNYILVNLAVASLFMVVFGFTVTFYSSLNGYFVLGPMGCAMEGFFATLG 1
2 GQVALWSLVVLAIERYIVVCKPMGNFRFASSHAIMGIAFTWIMALACAAPPLVGWSR 2
1 YIPEGLQCSCGPDYYTLNPDFHNESYVMYLFLVHFLLPIIIIFFTYGRLICKVKE 0
0 AAAQQQESASTQKAEKEVTRMVILMVIGFLTAWVPYASAAFWIFCNRGAEFTATLMTVPAFFSKSSCLFNPIIYVLLNKQ 0
0 FRNCMITTLCCGKNPLGDDDTSSAVSQSKTDVSSVSSSQVSPA* 0

>RHO2_geoAus Geotria australis lamprey rod RhB lamprey
0 MNGTEGANFYIPFHNRTGVVRSPYEYPQYYLADPWMYSAISAYVFTLILIGFPVNFMTLFVTFKLKKLRQPLNFILVNLCVADLLMIMFGFTTTFYTAMNGYFVFGPTGCNIEGFFATLG 1
2 GEVSLWSLVMLAIERYIVVCKPMGNFRFATTHAALGVVFTWVMASACAVPPLVGWSR 2
1 YIPEGMQCSCGPDYYTLNPKYYNESYVIYLFLVHFLLPVTIIFFTYGRLICTVKE 0
0 AAAQQQESASTQKAEREVTRMVIIMVVGFLVCWVPYASFAFYLFMNKGILFSATAMTVPAFFSKSSVLYNPIIYVLLNKQ 0
0 FRTCMVTTLFCGKNPFGEDDSSMVSTSKTEVSSVSSSQVSPS* 0

>SWS2_ornAna platypus blue cone bp 2 gene tandem -FLNB +MECP2 with MWS1 5 usual exons
0 MHKTHRNLQNELPEDFFIPLPLDTDNITSLSPFLVPQTHLGGSGIFMSLAAFMFLLITLGFPINLLTVICTIKYKKLRSHLNYILVNLAVSNMLVVCVGSATAFYSFAHMYFVLGPTACKIEGFAATLG 1
2 GMVSLWSLAVIAFERFLVICKPLGNLSFRGTHAIFGCAATWVFGLAASLPPLFGWSR 2
1 YIPEGLQCSCGPDWYTTNNKWNNESYVIFLFSFCFGVPLSIIIFSYGRLLLTLRA 0
0 VAKQQEQSATTQKAEREVTKMVIVMVLGFLVCWLPYASFSLWVVTNRGQVFDLRMASIPSVFSKASTIYNPIIYVFMNKQ 0
0 FRSCMLKLVFCGKSPFGDEDEISGSSQATQVSSVSSSQVSPA* 0

>SWS2_galGal chicken blue cone pigment galGal- ornAna+ homSap+ 
0 MHPPRPTTDLPEDFYIPMALDAPNITALSPFLVPQTHLGSPGLFRAMAAFMFLLIALGVPINTLTIFCTARFRKLRSHLNYILVNLALANLLVILVGSTTACYSFSQMYFALGPTACKIEGFAATLG 1
2 GMVSLWSLAVVAFERFLVICKPLGNFTFRGSHAVLGCVATWVLGFVASAPPLFGWSR 2
1 YIPEGLQCSCGPDWYTTDNKWHNESYVLFLFTFCFGVPLAIIVFSYGRLLITLRA 0
0 VARQQEQSATTQKADREVTKMVVVMVLGFLVCWAPYTAFALWVVTHRGRSFEVGLASIPSVFSKSSTVYNPVIYVLMNKQ 0
0 FRSCMLKLLFCGRSPFGDDEDVSGSSQATQVSSVSSSHVAPA* 0

>SWS2_taeGut Taeniopygia guttata
0 MPKPREMRDELPEDFYIPMSLETPNLTALSPFLVPQTHLGSPGIFKAMAAFMFLLVLLGVPINALTVLCTAKYKKLRSHLNYILVNLAVANLLVVCVGSTTAFYSFSQMYFALGPLACKIEGFTATLG 1
2 GMVSLWSLAVVAFERFLVICKPLGNFTFRGSHAVLGCAITWIFGLIASLPPLFGWSR 2
1 YIPEGLQCSCGPDWYTTDNKWNNESYVIFLFCFCFGFPLTVIVFSYGRLLLTLRA 0
0 VAKQQEQSASTQKAEREVTKMVVVMVLGFLVCWLPYCSFALWVVTHRGHPFDLGLASIPSVFSKASTVYNPIIYVFMNKQ 0
0 FRSCMLKLVFCGRSPFGDEDDVSGSSQATQVSSVSSSQVSPA* 0 

>SWS2_utaSta lizard
0 MHNSRPHSRDDLPEDFFIPMPLDVANITTLSPFLVPQTHLGSPALFMGMAAFMFLLIILGVPINVLTIFCTFKYKKLRSHLNYILVNLAVSNLLVVCIGSTTAFYSFAQMYFSLGPTACKIEGFAATLG 1
2 GMVSLWSLAVVAFERFLVICKPLGNFSFRGTHAIIGCIITWVFGLVASLPPLFGWSR 2
1 YIPEGLQCSCGPDWYTTNNKWNNESYVLFLFSFCFGVPLSVIIFSYGRLLLTLRA 0
0 VAKQQEQSATTQKAEREVTKMVVVMVMGFLVCWLPYASFALWVVTHRGEPFDVRLATIPSVFSKASSVYNPVIYVFMNKQ 0
0 FRSCMLKLVFCGKSPFGDEDDVSGSSQTTQVSSVSSSQVSPA* 0

>SWS2_xenTro Xenopus tropicalis
0 MSKGRPDLRMEMPDEFYVPIPLETTNISSLSPFLVPQTHLGTPGIFMSISAFMLFTIIFGFPLNLLTIICTVKYKKLRSHLNYILVNLAVANLIVICFGSTTAFYSFSQMYFSLGTLACKIEGFTATLG 1
2 GIIGLWSLAVVAFERFLVICKPMGNFTFRESHAVLGCILTWVIGLVAAIPPLLGWSR 2
1 YIPEGLQCSCGPDWYTVNNKWNNESYVLFLFCFCFGFPLAIIVFSYGRLLLALHA 0
0 VAKQQEQSATTQKAEREVTRMVIVMVVGFLVCWLPYASFALWAVTHRGELFDLRMSSVPSVFSKASTVYNPFIYIFMNRQ 0
0 FRSCMMKMIFCGKNPLGDDEETSVSGSTQVSSVSSSQIAPS* 0 

>SWS2_neoFor Neoceratodus forsteri (Australian lungfish)
0 MHRTKPDPQEDLPDDFYIPVSLNTNNITMLSPFLVPQTHLGSPSVFMVLSVFMFFLLITGIPINVLTIICTFKYKKLRSHLNYILVNLAVANLIVVGFGSTTAFYSFSQMYFAWGPLACKIEGFAATLG 1
2 GMVSLWSLAVVAFERFLVICKPLGNFTFRSTHAIIGCVATWVFGLISSAPPLFGWSR 2
1 YIPEGLQCSCGPDWYTTNNKWNNESYVIFLFCFCFGFPLSVIIFSYGRLLMTLRA 0
0 VAKQQEQSASTQKAEREVTKMVVVMVLGFLVCWLPYTVFSLWVVTHRGESFELALGSIPAVFSKSSTVYNPLIYVFMNKQ 0
0 FRSCMMKLIFCGKSPFGDEDDASSASQSTQVSSVSSSQVAPA* 0

>SWS2_takRub Takifugu rubripes
0 MRGVRQHEFQEDFYIPIPLDVDNITALSPFLVPQDHLGSPAVFYGMSAFMFFLFVAGTGINVLTIACTIQYKKLRSHLNYILVNLAFSNLLVTTVGSFTCFCCFFVRYMIVGPLGCKIEGFAATLG 1
2 GMVSLWSLAVVAFERWLVVCKPLGNFIFKPDHAIVCCIFTWFFALIISAPPLFGWSR 2
1 YIPEGFQCSCGPDWYTTGNKYNNESYVWFIFGFGFAVPLFVIVFCYSQLLVMLKS 0
0 AKAQAESASTQKAEREVTRMVVVMILGFLVCWLPYASFALWVVNNRGTPFDLRLATIPACFSKASTVYNPIIYVVLNKQ 0
0 FRSCMKKMLGMSGGDDEESSSQSVTEVSKVSPS* 0 

>SWS2_gasAcu Gasterosteus aculeatus (stickleback) 359 aa
0 MKHGRVPEIPEDFYIPISLDTDNITSLSPFLVPQDHLASKATFYSLAFYMFFILIVGTFINALTVACTVQNKKLRSHLNYILVNLAVSNLLVSGVGAFTAFLSFAARYFVLGTLACKVEGFLATLG 1
2 GMVSLWSLAVIAFERWLVICKPLGNFIFKPDHALVCCAFTWVFALAASAPPLVGWSR 2
1 YIPEGLQCSCGPDWYTTNNKYNNESYVLFLFGFCFAVPFCTICFCYSQLLFTMKMA 0
0 AKAQAESASTQKAEREVTRMVVLMVMGFLVCWMPYASFALWVVNNRGQTFDLRFASIPSVFSKSSAVYNPVIYVLLNKQ 0
0 FRSCMMKMLGMGGGDDEESSTSSVTEVSKVGPA* 0

>SWS2_geoAus Geotria australis lamprey blue-sensitive retinal pigment lamprey
0 MYQGKSTQVDDLPEDFYIPIALNVKNMSELSPFLVPQVHLGDSFIFYGMSAFMLFLVLAGFPLNFLTVFVTIKYKKLRSHLNYILVNLAIANLIVVCCGSTLAFYSFMHKYFILGPLFCKMEGFTATLG 1
2 GMLSLWSLAVLAFERCLVICKPFGNIAFRGTHALIRCGFAWAAAIAASTPPLFGWSR 2
1 YIPEGLQCSCGPDWYTTNNKYNNESYVMFLFIFCFGTPFTIIIVSYSKLILTLRA 0
0 AAAQQQESASTQKAEKEVSRMVVIMVGGFLVCWLPYASLALWIVFNRGSPFDLRLATIPSVFSKASTVYNPVIYIFLNKQ 0
0 FRSCMMKTIFCGKNPLGDDEDATSTTTQVSSVSTSQVAPA* 0

>SWS1_homSap 5 exons all GT-AG Blue opsin chr7:128,199,783-128,203,087 7q32.1 - 3305 5 348 (tritanopia) [MIM:190900].
0 MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVA 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNPIIYCFMNKQ 0
0 FQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN* 0

>SWS1_monDom Monodelphis domesticus
0 MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHFQTVFMGFVFCAGTPLNAVVLVATLRYKKLRQPLNYILVNVSLCGFIFCIFAVFTVFISSSQGYFIFGRHVCAMEAFLGSVA 1
2 GLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWVIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIMPLFLICFSYSQLLRALRA 0
0 VAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNQNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FHACIMEMVCRKPMTDDSDVSSSQKTEVSAVSSSQVGPT* 0

>SWS1_galGal chicken violet cone pigment
0 MSSDDDFYLFTNGSVPGPWDGPQYHIAPPWAFYLQTAFMGIVFAVGTPLNAVVLWVTVRYKRLRQPLNYILVNISASGFVSCVLSVFVVFVASARGYFVFGKRVCELEAFVGTHG 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFSSRHALLVVVATWLIGVGVGLPPFFGWSR 2
1 YMPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLIIFSYSQLLSALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRDHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FRACIMETVCGKPLTDDSDASTSAQRTEVSSVSSSQVGPT* 0

>SWS1_taeGut Taeniopygia guttata
0 MDEEEFYLFKNQSSVGPWDGPQYHIAPMWAFYLQTIFMGLVFVAGTPLNAIVLIVTIKYKKLRQPLNYILVNISVSGLMCCVFCIFTVFIASSQGYFVFGKHMCAFEGFAGATG 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFNSRHALLVVAATWIIGVGVAIPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYKSEYYTWFLFIFCFIVPLSLIIFSYSQLLSALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCMCYVPYAALAMYMVNNREHGIDLRLVTIPAFFSKSSCVYNPIIYCFMNKQ 0
0 FRACIMETVCGRPMTDDSEVSSSAQRTEVSSVSSSQVGPS* 0

>SWS1_anoCar Anolis carolinensis (lizard)
0 MSGQEDFYLFENISSVGPWDGPQYHIAPMWAFYFQTAFMGFVFFAGTPLNAIILIVTVKYKKLRQPLNYILVNISFAGFLFCTFSVFTVFMASSQGYFFFGRHVCAMEAFLGSVA 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFNSRHALLVVAATWIIGVGVAIPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYKSEYYTWFLFIFCFIVPLTLIIFSYSQLLGALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYASLAMYMVNNRDHGLDLRLVTIPAFFSKSSCVYNPIIYCFMNKQ 0
0 FRACILETVCGKPMSDESDVSSSAQKTEVSSVSSSQVSPS* 0

>SWS1_utaSta Uta stansburiana
0 MSGEEDFYLFENISSVGPWDGPQYHIAPMWAFYFQTAFMGFVFFAGTPLNAIILIVTVKYKKLRQPLNYILVNISFAGFLFCVFSVFTVFLASSQGYFFFGRHICALEAFLGSVA 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFNSKHALLVVAATWFIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYKSEYYTWFLFIFCFIVPLTLIIFSYSQLLGALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRDHGIDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FRACIMETVCGKPMTDESDVSSSAQKTEVSSVSSSQVSPS* 0

>SWS1_xenLae Xenopus laevis
0 MLEEEDFYLFKNVSNVSPFDGPQYHIAPKWAFTLQAIFMGMVFLIGTPLNFIVLLVTIKYKKLRQPLNYILVNITVGGFLMCIFSIFPVFVSSSQGYFFFGRIACSIDAFVGTLT 1
2 GLVTGWSLAFLAFERYIVICKPMGNFNFSSSHALAVVICTWIIGIVVSVPPFLGWSR 2
1 YMPEGLQCSCGPDWYTVGTKYRSEYYTWFIFIFCFVIPLSLICFSYGRLLGALRA 0
0 VAAQQQESASTQKAEREVSRMVIFMVGSFCLCYVPYAAMAMYMVTNRNHGLDLRLVTIPAFFSKSSCVYNPIIYSFMNKQ 0
0 FRGCIMETVCGRPMSDDSSVSSTSQRTEVSTVSSSQVSPA* 0

>SWS1_neoFor Neoceratodus forsteri (Australian lungfish)
0 MSGEEEFYLFKNISSVGPWDGPQYHIAPKWAFFLQAAFMGFVLFVGTPLNAIVLFVTIKYKKLQQPLNYILVNISLAGFIFCFFGVFAVFIASCQGYFIFGKTVCALEGFTGSVA 1
2 GLVTGWSLAILAFERYLVICKPIGNFRFGSKHSMIAVVAAWVIGVGVSIPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYKSEYYTWFLFIFCFIIPLFIICFSYSQLLGALRA 0
0 VAAQQQESATTQKAEREVSRMIIVMVGSFCVCYVPYAALAMYMVNNRDHGIDLRLVTIPAFFSKSSFVYNPIIYCFMNKQ 0
0 FRACIMQTVFGKPMTDDSDISSSGKTEVSSVSSSQVNPS* 

>SWS1_danRer Danio rerio
0 MDAWAVQFGNASKVSPFEGEQYHIAPKWAFYLQAAFMGFVFIVGTPMNGIVLFVTMKYKKLRQPLNYILVNISLAGFIFDTFSVSQVSVCAARGYYSLGYTLCSMEAAMGSIA 1
2 GLVTGWSLAVLAFERYVVICKPFGSFKFGQGQAVGAVVFTWIIGTACATPPFFGWSR 2
1 YIPEGLGTACGPDWYTKSEEYNSESYTYFLLITCFMMPMTIIIFSYSQLLGALRA 0
0 VAAQQAESESTQKAEREVSRMVVVMVGSFVLCYAPYAVTAMYFANSDEPNKDYRLVAIPAFFSKSSSVYNPLIYAFMNKQ 0
0 FNACIMETVFGKKIDESSEVSSKTETSSVSA* 0

>SWS1_oryLat Oryzias latipes
0 MGKYFYLYENISKVGPYDGPQYYLAPTWAFYLQAAFMGFVFFVGTPLNFVVLLATAKYKKLRVPLNYILVNITFAGFIFVTFSVSQVFLASVRGYYFFGQTLCALEAAVGAVA 1
2 GLVTSWSLAVLSFERYLVICKPFGAFKFGSNHALAAVIFTWFMGVGCACPPFFGWSR 2
1 YIPEGLGCSCGPDWYTNCEEFSCASYSKFLLVTCFICPITIIIFSYSQLLGALRA 0
0 VAAQQAESASTQKAEKEVSRMIIVMVASFVTCYGPYALTAQYYAYSQDENKDYRLVTIPAFFSKSSCVYNPLIYAFMNKQ 0
0 FNGCIMEMVFGKKMEEASEVSSKTEVSTDS*0

>SWS1_geoAus Geotria australis lamprey UV-sensitive retinal pigment lamprey
0 MSGDEEFYLFKNISKVGPWDGPQFHIAPKWAFYLQAAFMGFVFICGTPLNAIVLVVTIKYKKLRQPLNYILVNISAAGLVFCLFSISTVFVASMQGYFFLGPTICALEAFFGSLA 1
2 GLVTGWSLAFLAAERYIVICKPFGNFRFGSKHALVAVGLTWMLGLSVALPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYKSEYYTYFLFVFCFVVPLSIIIFSYGSLLGTLRA 0
0 VAAQQQESASTQKAEREVSRMVIMMVASFCTCYVPYAALAVYMVTNRDHNIDLRFVTVPAFFSKASCVYNPLIYSFMNKQ 0
0 FRACILETVCGKPITDESETSSSRTEVSSVSTTQMIPG* 0

>LWS_homSap OPN1MW NP_000504 length=364
0 MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTR 1
2 GPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFVLGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRA 0
0 VAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVIYVFMNRQ 0
0 FRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA* 0

>LWS_monDom OPN1MW NP_000504 length=364 macEug for last exon
0 MTQAWDPAGFLARRRDVNEDDNDETTRSSLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETVIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMATCCIFPLSIILLCYVQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYSFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0 

>LWS_ornAna platypus LWS green cone -Ultra401:228,567-238,486
0 MTPAWNSGVYAARRRFEDEEDTTRTSVFVYTNSNNTR 1
2 DPFEGPNYHIAPRWAYNVTSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLSIISWERWIVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIVLCYLQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTIFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIMQLFGKKVDDGSELSSTSRTEVSSVSSVSPA* 0

>LWS_galGal chicken green iodopsin red cone long-wave-sensitive missing in assembly
0 MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGHPMCVVEGYTVSAC 1
2 GITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVSLAIRA 0
0 VAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVSPA* 0

>LWS_anoCar Anolis
0 MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNITSVWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISGYFILGHPMCVLEGYTVSTC 1
2 GISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSWVWSAVWTAPPVFGWSR 2
1 YWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILLCYLQVWLAIRA 0
0 VAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIMQLFGKKVDDGSELSSTSRTEVSSVSNSSVSPA* 0

>LWS_xenTro Xenopus tropicalis (frog) NM_001102861
0 MASHWNEAVFAARRRNDDDDTTRSSVFTYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNISSLWMIFVVLASVFTNGLVLVATLKFKKLRHPLNWILVNMAIADLGETVIASTISVCNQIFGYFVLGHPMCILEGYTVSVC 1
2 GIAALWSLTVIAWERWFVVCKPFGNIKFDGKLAATGIIFSWVWAAGWCAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMLVLMITCCIIPLAIIVLCYMHVWLTIRQ 0
0 VAQQQKESESTQKAEREVSRMVVVMIIAYIFCWGPYTFFACFAAFNPGYNFHPLAAAMPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIYQLFGKKVDDGSEVSSTSRTEVSSVSNSSVSPA* 0

>LWS_neoFor Neoceratodus forsteri (Australian lungfish)
0 MAEPWDAVLAARRRHQDEETTRSTIFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMIFVVFASCFTNGLVLMATYKFKKLRHPLNWILVNLAIADLGETLIASTISVTNQIFGYFILGHPMCMLEGFTVATC 1
2 GITGLWSLTIIAWERWVVVCKPFGNIKFDGKWAAGGIIFSWVWSAFWCAMPLFGWSR 2
1 FWPHGLKTSCGPDVFSGEDKYGTRSFMIALMITCCIIPLGVIILCYIQVWWAIRT 0
0 VAKQQKESESTQKAEKEVSRMVVVMIFAYCFCWGPYTFMACFGAAYPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIYQLLGKKVDDGSELSSTSKTEVSSVSNSSVSPA* 0

>LWS_takRub Takifugu rubripes (pufferfish)
0 MAEEWGKQSFAARRYHEDTTRGSAFVYTNSNHTR 1
2 DPFEGPNYHIAPRWVYNVATVWMFIVVVLSVFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVFASTISVCNQFFGYFILGHPMCVFEGYTVSTC 1
2 GIAALWSLTIISWERWVVVCKPFGNVKFDAKWATGGIVFSWVWAAVWCAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMITCCIIPLAIIILCYLAVWLAIRS 0
0 VAMQQKESESTQKAEKEVSRMVVVMIVAYCVCWGPYTFFACFAAANPGYAFHPLAAAMPAYFAKSATIYNPVIYVFMNRQ 0
0 FRVCIMKLFGKEVDDGSEVSTSKTEVSSVAPA* 0

>LWS_gasAcu Gasterosteus aculeatus
0 MAEEWGKQAFAARRYNEDTTRGSMFVYTNSNNTK 1
2 DPFEGPNYHIAPRWVYNLSTLWMFIVVALSVFTNGLVLVATAKFKKLQHPLNWILVNLAIADLGETVFASTISVCNQFFGYFILGHPMCVFEGYVVSVC 1
2 GITALWSLTIISWERWIVVCKPFGNVKFDAKWATAGIVFSWIWSAVWCAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMITCCLIPLAIIILCYLAVWLAIRA 0
0 VAMQQKESESTQKAERDVSRMVVVMIVAYIVCWGPYTTFACFAAANPGYAFHPLAAAMPAYFAKSATIYNPVIYVFMNRQ 0
0 FRSCIMQLFGKEVDDGSEVSTsKTEVSSVAPA* 0

>LWS_petMar Petromyzon maritimus lamprey traces key to intron 3 position and gapping
0 MTASWQGAMFAARRRQDDEDTTMESLFRYTNENNTK 1
2 DPFEGPNYHIAPRWVFNLTSVWMIIVVVLSLFSNGLVLVATVKFKKLRHPLNWIIVNLAIADILETIFASTISVCNQVYGYFILGHPMCVFEGYVVSTC 1
2 GIAGLWSLAIISWERWMVVCKPFGNIKFDGKIATILIVFSWVWPASWCSLPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSTDPGVQSYMVVLMITCCFLPLSIIILCYLQVWLAIHS 0
0 VAQQQKESETTQKAERDVSRMVVVMILAYVFCWGPYTFFACFAAANPGYSFHPIAAALPAYFAKGATIYNPIIYVFMNRQ 0
0 FRNCILQLFGKKVDDGSEVSSSSRTEVSSVSNSSVSPA* 0

>LWS_letJap lamprey Lethenteron japonicum
0 MTASWHGAVFAARRRNDDEDTTKDSIFRYTNENNTR 1
2 DPFEGPNYHIAPRWMFNLTSVWMIIVVVLSLFTNGLVLVATMKFKKLRHPLNWILVNLAIADILETIFASTISVCNQVFGYFILGHPMCVFEGYVVSTC 1
2 GIAGLWSLAIISWERWMVVCKPFGNIKFDGKIAIILIVFSWVWPACWCSLPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFLPLSVIILCYLQVWLAIHS 0
0 VAQQQKESETTQKAERDVSRMVVVMILAYIFCWGPYTFFACYAAANPGYAFHPLTAALPAYFAKSATIYNPVIYVFMNRQ 0
0 FRNCIMQLFGKKVDDGSEVSSASRTEVSSVSNSSISPA*

>LWS_geoAus Geotria australis lamprey red-sensitive retinal pigment 
0 MAQSWERAMFAARRRQDEDTTKGDLFRYTNENNTR 1
2 DPFEGPNYHIAPRWMYNLTSFWMIIVVILSLFTNGLVLVATLKFKKLRHPLNWILVNLAIADIGETIFASTVSVVNQIFGYFILGHPLCVFEGFTVSVC 1
2 GITALWSLAIISFERWMVVCKPFGNLKFDGKVAIVLIIFSWAWSAGWCAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSTDPGVQSYMVVLMITCCFIPLALIIICYLQVWLAIHT 0
0 VAQQQKESETTQKAERDVSRMVVVMIFAYIFCWGPYTFFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIMQLFGKKVDDGSEVSSSARTEVSSVSNSSVSPA* 0

>PIN_galGal pinopsin pineal pigment non-visual homSap- RPH3AL DOC2B PIN TEX14 RAD51C
0 MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLT 1
2 GIVGLWSLAILALERYVVVCRPLGDFQFQRRHAVSGCAFTWGWALLWSTPPLLGWSSYVPE 1
2 GLRTSCGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRA 0
0 AAAQQKEADTTQRAEREVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVFMNKQ 0
0 FQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV* 0

>PIN_utaSta Uta stansburiana pinopsin missing in Anole genome
0 MVNEWSNATPGPFDGPQWPYLAPRSIYTSVAVLMGLVVVSAAFVNGLVIVVSIQYKKLRSPLNYILVNLAIADLLVTSFGSTLSFANNIYGFFVLGQTACEFEGFMVSLT 1
2 GIVGLWSLAILAFERYLVICKPVGDFRFQQRHAVFGCVFTWMWSLVWTLPPLFGWSSYVPE 1
2 GLRTSCGPNWYTGGSGNNSYIMALFVTCFALPLGMIIFSYASLLLTLRA 0
0 VATQQKEVETTQQAEKEVTRRVIAMVMAFLVCWLPYASFAMVVATNKDLVIQPALASLPSYFSKTATVYNPIIYVFMNKQ 0
0 FRSCLLSTMSCGHRPRGAQETTPAMISIPQGPTSALQGSRNKVTPSASEGSGNEAIPS* 0

>PIN_pheMad Phelsuma madagascariensis gekko
0 MHVQMANASQASLKNGTLSPFDGPQWPHRASRRVYTSLAALMGVVVLSASLANGLVIAVSVRFKRLRSPLNYILVNLATADLLVTFFGSIISFVNNAVGFFVFGKTACRFEGFMVSLT 1
2 GIVGLWSLAILAFERYLVICKPVGDFQFQRRHAVIGCLYTWGWSLIWTVPPLFGWSSYVPE 1
2 GLGTSCGPNWYMGGTNNNSYIVALFVTCFALPLSMILFSYANLLLTLRA 0
0 VAAQQKEQETTQRAEKEVTRMVITMVMAFLVCWLPYATFAMVVATTKDLSIQPGLASLPSYFSKTATVYNPIIYVFMNKQ 0
0 FRSCLLNTVSCGRIPQTMPGTPATTAVRGGFVLTSEGRGNKVASTELHS* 0

>PIN_podSic Podarcis sicula pinopsin mRNA ruin lizard
0 MQASNASWVEVRNRTPGPFEGPQWPYLAPQSTYISVAVLMGLVVISATLVNGLVIVVSVQFKKLRSPLNYVLVNLAVADLLVTFFGSTISFVNNAQGFFIFGQATCEFEGFMVSLT 1
2 GIVGLWSLAILAFERYLVICKPVGDFRFPARHAVLGCAFTWGWSFVWTVPPLLGWSSYVPE 1
2 GLRTSCGPNWYSGGSSNNSYIMTLFVTCFAMPLSTILFSYANLLMTLRT 0
0 VAAQQKEQETTQRAEREVTRMVVAMVAAFLVCWLPYASFAMVVATHKDLAIRPALASLPSYFSKTATVYNPIIYVFMNKQ 0
0 FRSCLLYKMSCGHRALSSQDTTPAGISLPGRLTTSASKGSRNQVSPS* 0

>PIN_xenTro Xenopus tropicalis
0 MRAGNMSAYEAPGPYDGPQWPHLAPRSTFLTVAAVMCMVVILAFFVNGLVIVVTLKYKKLRSPLNYILVNLAIANLLVTIFGSSVSFSNNVVGYFFMGKTMCEFEGFMVSLT 1
2 GIVGLWSLAILAFERYLVICKPMGDFRFQQKHAILGCSFTWVWSFIWTSPPLFGWCSYVPE 1
2 GLRTSCGPNWYTGGTNNNSYIMALFLTCFIMPLSTIIFSYSNLLMALRA 0
0 VAAQQKDSETTQRAEKEVTRMVIAMVLAFLICWLPYASFAVVVAVNKDVVIEPTVASLPSYFSKTATVYNPIIYVFMNKQ 0
0 FRNCLMTLLCCGRSFGDDETSSASGRTDVTSVSEAGGNKVTPA* 0

>PIN_bufJap Bufo japonicus toad classifies somewhat oddly
0 MHSANMSALETPGPFEGPQWPHVAPRSTYLTVAVLMGMVVFLAFFVNGMVIVVSLKYKKLRSPLNYILVNLAVADILVTMFGSTVSFHNNIFGFFTLGKLVCELEGFVVSLT 1
2 GIVGLWSLAILAFERYIVICKPMGDFRFQQRHAVMGCAFTWIWAFLWTSPPLIGWCSYVPE 1
2 GLGTSCGPNWYTGGTNNNSYILALFTTCFMMPLTTIIFSYSNLLLALRA 0
0 VAAQQKESETTQRAEREVTRMVIAMVLAFLICWLPYAVFAIVMASNKNVVIDPTLASMPSYFSKTATVYNPVIYVFMNKQ 0
0 FRDCLTKLLCCGRNPFGEDETSTTSGRTDVTSVSEGGGNKVTPA* 0

>VAOP_galGal Gallus gallus exon 1 genbank error + too short + frameshift INPP5A NKX6 VAOP ALDH18A stubbed in terminal finch
0 MDVFRALGNESLLSNSSGPARWDPFHHPLDSIQPWHFRLVAAVMFVVTSLSLAENLAVILVTFKFKQLRQPVNYVIVNLSVADFLVSLTGGTISFLANLKGYFYMGHWACVLEGFAVTFF 1
2 GIVALWSLALLAFERYIVICRPVGNMRLRGKHAAQGIAFVWTFSFIWTIPPTMGWSSYTTSKIGTTCEPNW 2
1 YSGAYNDRSYIIAFFTTCFIVPLLVILVSYGKLLQKLRK 0
0 VSNTQGRLRTARKPERQVTRMVVVMIIAFLICWMPYAVFSILATAYPSIELDPHLAAIPAFFSKTATVYNPIIYVFMNKQ 0
0 FRMCLIQMFKCSAIETAESNMNPTSERATLTQDKRDSQLSVMAVRSTILKRKTGDEHRADDLWLFRQLQKPKCVPCRAGDGS* 0

>VAOP_anoCar Anole INPP5A NKX6 VAOP new
0 MAGLRREAENDSWLFDPSSSSAPFDPFLQPLDIIEPWNFHLISALMFVVTLFSLSENFTVILVTIKFKQLRQPLNYVIVNLSVADFLVSLIGGTISFSTNLKGYFYMGHWACVLEGFAVTFF 1
2 GIVALWSLALLAFERYVVICRPLGNMRLNGKHAALGVAFVWIFSFIWTVPPTMGWSSYTTSKIGTTCEPNW 2
1 YSGDYNDHTFIITFFTTCFILPLLVILVSYGKLMRKLRK 0
0 VSDTQGRLGTTRKPERQVTGMVVIMILAFLICWSPYAAFSILVTACPSIELDPRLAAIPAFFSKTATVYNPVIYVFMNNQ 0
0 FRKCLVQLFQCSSQETMDANVNPISEKDTLTHTKHCGEMSTVAAHVIVFNPRSEDEQGSCQSFAQLAISENKVYPL* 0

>VAOP_xenTro frog new lost synteny GSTO1 VAOP C10ORF92
0 MPTNVSLLATPENSTVWNPFTGPLKTIEAWNFHLLAALMFVVTSLSIAENFIVILVTAKFKQLRQPLNYIIVNLSVADFLVSVIGGTISIATNSRGYFYLGSWACVLEGFAVTFF 1
2 GIVALWSLSVLAFERYIVICRPLGNLRLQGKHSALAIIFVWVFSFVWTIPPTMGWSSYTTSKIGTTCEPNW 2
1 YSGEMRDHTYIITFLTTCFVFPLLVIFMSYGKLMRKLRK 0
0 VSDTQGRLGSTRKPEKEVTRMVVIMILAFLICWTPYAAFSILITAHPTIDLDPRLAAIPAFFAKTASMYNPIIYVYMNKQ 0
0 FRRCLYQMFNINDPEAKESNLNPTSERGVLTRNNNGGEMLAIATHITSSAVTNREEEKSSSNSFAHIPVSDNKVCPM*

>VAOP_danRer Danio rerio vertebrate ancient long opsin assembly missing exon 3 no synteny
0 MEASSAAVNAVSPAEDPFSAPLSSIAPWNYSVLAALMFVVTALSLSENFTVMLVTFRFQQLRQPLNYIIVNLSLADFLVSLTGGSISFLTNYHGYFFLGKWACVLEGFAVTFF 1
2 GIVALWSLAVLAFERFFVICRPLGNIRLRGKHAALGLVFVWSFSFIWTVPPVLGWSSYTVSRIGTTCEPNW 2
1 YSGNFHDHTFIITLFSTCFIFPLGVIIVCYCKLIRKLRK 0
0 VSNTHGRLGNARKPERQVTRMVVVMIVAFMVAWTPYAAFSIIITAHPSMHVDPRLAAIPAFVAKTAAVYNPIIYVFMNKQ 0
0 FRKCLVQLLSCSKVTVVEGNNNQTTERAGMTSGSNTGEMSAIAARVSVPKTEENPGDRSTFSHIPIPENKVCPM*

>VAOP_takRub Takifugu rubripes vertebrate ancient opsin
0 MESLSLSVNGVSYTVAAELAPTNDPFTGPINNIAQWNFTILAVLMFVVTSLSLCENFLVMFITFKFKQLRQPLNYIIVNLAIADFLVSLTGGLISFLTNARGYFFLGRWACVLEGFAVTYF 1
2 GIVAMWSLAVLSFERFFVICRPLGNMRLQAKHAAIGLLFVWTFSFVWTFPPVLGWNRYTVSKIGTTCEPDW 2
1 YSNNMTSHSYIITFFSTCFILPLGIIFFCYGKLLRKLRK 0
0 VSHGRLATARKPERQVTRMVVVMIVAFMVAWTPYATFAILVTIHPTIELDPR
0 FRKCLIQHFIGMGVMAESNMNPTSERPGITAESQTGEMSAIAARVPVGATAALHSDGSPTDCGSLAQLPIPENKVCPI* 0

>VAOP_rutRut Rutilus rutilus (roach minnow) vertebrate ancient opsin
0 MELFPVAVNGVSHAEDPFSGPLTFIAPWNYKVLATLMFVVTAASLSENFAVMLVTFRFTQLRKPLNYIIVNLSLADFLVSLTGGTISFLTNYHGYFFLGKWACVLEGFAVTYF 1
2 GIVALWSLAVLAFERFFVICRPLGNIRLRGKHAALGLLFVWTFSFIWTIPPVLGWSSYTVSKIGTTCEPNW 2
1 YSGNFHDHTFIIAFFITCFILPLGVIVVCYCKLIKKLRK 0
0 VSNTHGRLGNARKPERQVTRMVVVMIVAFMVAWTPYAAFSIVVTAHPSIHLDPRLAAAPAFFSKTAAVYNPVIYVFMNKQ 0
0 FRKCLVQLLRCRDVTIIEGNINQTSERQGMTNESHTGEMSTIASRIPKDGSIPEKTQEHPGERRSLAHIPIPENKVCPM* 0

>VAOP_petMar Petromyzon marinus 5 exons validated #123 in traces pineal gland-specific opsin AH006524
0 MDALQESPPSHHSLPSALPSATGGNGTVATMHNPFERPLEGIAPWNFTMLAALMGTITALSLGENFAVIVVTARFRQLRQPLNYVLVNLAAADLLVSAIGGSVSFFTNIKGYFFLGVHACVLEGFAVTYF 1
2 GVVALWSLALLAFERYFVICRPLGNFRLQSKHAVLGLAVVWVFSLACTLPPVLGWSSYRPSMIGTTCEPNW 2
1 YSGELHDHTFILMFFSTCFIFPLAVIFFSYGKLIQKLKK 0
0 ASETQRGLESTRRAEQQVTRMVVVMILAFLVCWMPYATFSIVVTACPTIHLDPLLAAVPAFFSKTATVYNPVIYIFMNKQ 0
0 FRDCFVQVLPCKGLKKVSATQTAGAQDTEHTASVNTQSPGNRHNIALAAGSLRFTGAVAPSPATGVVEPTMSAAGSMGAPPNKSTAPCQQQGQQQQQQGTPIPAITHVQPLLTHSESVSKICPV* 0

>PPIN_anoCar Anoles parapinopsin PPIN syntenic region deleted in chicken
0 MDSLDTNTLSPNASTVRVVLMPRIGYTIIAIIMATSCTLSVILNTAVIAITIKYRQLRQPINYSLVNLAIADLGAALLGGSLNVETNAVGYYNLGRVGCVTEGFAMAFF 1
2 GIVALCTIAVIAVDRAIVIAKPMGTITFTTRKAMIGVAVSWIWSLVWNTPPLFGWGGYQMEGVMTSCAPDWANSDPINVSYIICYFLFCFTIPFITILASYGYLIWTLRQ 0 
0 VAKVGLAQRGSTTKAEAQVSRMVIVMVMAFLICWLPYATFALVVVGNPQIYINPIIATIPMYMAKSSTFYNPIIYIFMNKQ 0
0 FRDCLVRCLLCGRNPCASEQTDEDDLEVSTIAPAPSSRRGKVAPV* 0

>PPIN_xenTro Xenopus tropicalis bistable UV pigment lamprey pineal broken contigs ACTR8 SELK PPIN CACNA2D3 genome only last 2
0 MADEALLPPMMNVTNEEMHPGKVLMPRIGYTILALIMAVFCAAALFLNVTVIVVTFKYRQLRHPINYSLVNLAIADLGVTVLGGALTVETNAVGYFNLGRVGCVIEGFAVAFF 1
2 GIAALCTIAVIALDRVFVVCKPMGTLTFTPKQALAGIAASWIWSLIWNTPPLFGWGSYELEGVMTSCAPNWYSADPVNMSYIVCYFSFCFAIPFLIIVGSYGYLMWTLRQ 0
0 VAKLGVAEGGTTSKAEVQVSRMVIVMILAFLVCWLPYAAFAMTVVANPGMHIDPIIATVPMYLTKTSTVYNPIIYIFMNKQ 0
0 FQECVIPFLFCGRNPWAAEKSSSMETSISVTSGTPTKRGQVAPA* 0

>PPIN_ictPun Ictalurus punctatus (channel catfish) parapinopsin index sequence
0 MASIILINFSETDTLHLGSVNDHIMPRIGYTILSIIMALSSTFGIILNMVVIIVTVRYKQLRQPLNYALVNLAVADLGCPVFGGLLTAVTNAMGYFSLGRVGCVLEGFAVAFF 1
2 GIAGLCSVAVIAVDRYMVVCRPLGAVMFQTKHALAGVVFSWVWSFIWNTPPLFGWGSYQLEGVMTSCAPNWYRRDPVNVSYILCYFMLCFALPFATIIFSYMHLLHTLWQ 0
0 VAKLQVADSGSTAKVEVQVARMVVIMVMAFLLTWLPYAAFALTVIIDSNIYINPVIGTIPAYLAKSSTVFNPIIYIFMNRQ 0
0 FRDYALPCLLCGKNPWAAKEGRDSDTNTLTTTVSKNTSVSPL* 0

>PPIN_danRer Danio rerio parapinopsin [not checked wgd or synteny]
0 MESETSTAASGSIAEVMPRMGYTILAVIIGVFSVCGVILNVTVITVTLKYKQLRQPLNFALVNLAVADLGCAVFGGLPTVVTNAMGYFSLGRVGCVLEGFAVAFF 1
2 GIAALCSVAVIALERCMVVCRPVGSISFQTRHAVFGVAVSWLWSFIWNTPPLFGWGRLQLEGVRTSCAPDWYSRDLANVSFIVCYFLLCFALPFSVIVYSYTRLLWTLRQ 0
0 VSRLQVCEGGSAARAEAQVSCMVVVMILAFLLTWLPYASFALCVILIPELYIDPVIATVPMYLTKSSTVFNPIIYIFMNRQ 0
0 FRDRALPFLLCGRNPWAAEAEEEEEETTVSSVSRSTSVSPA* 0

>PPIN_oncMyk Oncorhynchus mykiss
0 MDHQQLLPNLHGNISSSPGSVSEALLSRTGFTILAVIIGVFSVSGVCMNVLVIMVTMRHRKLRQPLNYALVNLAVADLGCALFGGLPTMVTNAMGYFSMGRLGCVLEGFAVAFF 1
2 GIAGLCSVAVIAVDRYVVVCRPMGAVMFQTRHAVGGVVLSWVWSFLWNTPPLFGWGSFELEGVRTSCSPNWYSREPGNMSYIILYFLLCFAIPFSIIMVSYARILFTLHQ 0
0 VSKLKVLEGNSTTRVEIQVVRMVVVMVMAFLLSWLPYAAFALSVILDPSLHINPLIATVPMYLAKSSTVYNPIIYVFMNRQ 0
0 FRDCAVPFLLCGLNPWASEPVGSEADTALSSVSKNPRVSPQ*

>PPIN_petMar Petromyzon maritimus lamprey trace-validated introns bistable pineal UV/green 
0 MENLTSLDLLPNGEVPLMPRYGFTILAVIMAVFTLASLVLNSTVIIVTLRHRQLRHPLNFSLVNLAVADLGVTVFGASLVVETNAVGYFNLGRVGCVIEGFAVAFF 1
2 GIAALCTIAVIAVDRFVVVCKPLGTLMFTRRHALLGITWAWLWSFVWNTPPLFGWGSYKLEGVRTSCAPDWYSRDPANVSYIVSFFSFCFAIPFLVIVVAYGRLLWTLHQ 0
0 VAKLGMGESGSTAKAEAQVSRMVVVMVVAFLVCWLPYALFAMIVVAKPGVYIDPVIATLPMYLTKTSTVYNPIIYIFMNRQ 0
0 FRDCAVPFLLCGRNPWAEPSSESATTASTSATSVTLASVPGQVSPS* 0

>PPIN_letJap Lethenteron japonicum lamprey AB116380 bistable pineal UV/green aligns perfectly
0 MENLTSLDLLPNGEVPLMPRYGFTILAVIMAVFTIASLVLNSTVVIVTLRHRQLRHPLNFSLVNLAVADLGVTVFGASLVVETNAVGYFNLGRVGCVIEGFAVAFF 1
2 GIAALCTIAVIAVDRFVVVCKPLGTLMFTRRHALLGIAWAWLWSFVWNTPPLFGWGSYELEGVRTSCAPDWYSRDPANVSYITSYFAFCFAIPFLVIVVAYGRLMWTLHQ 0
0 VAKLGMGESGSTAKAEAQVSRMVVVMVVAFLVCWLPYALFAMIVVTKPDVYIDPVIATLPMYLTKTSTVYNPIIYIFMNRQ 0
0 FRDCAVPFLLCGRNPWAEPSSESATAASTSATSVTLASAPGQVSPS* 0

>PPINa_cioInt Ciona intestinalis parapinopsin 8 mostly odd exons 88 +- 200671 202490 1820 opsin1 larval ocellus
0 MNQWLETIMNERKFEIVNSSLQG 2
1 LLKPDSLGMDHDVTPTVDLTDGVPQCKDLNPYVLKGDGWVPQHISRANRSTYSFLCVYMTFVFLLSCSLNILVIVATLKNK 0
0 VLRQPLNYIIVNLAVVDLLSGFVGGFISIAANGAGYFFWGKTMCQIEGYFVSNFGVTGLL 0
0 SIAVMAFERYFVICKPFGPVRFEEKHSIFGIV 0
0 ITWVWSMFWNTPPLIFWDGYDTEGLGTSCAPNWFVKEKRERLFIILYFVFCFVIPLAVIMICYGKLILTLRQ 0
0 IAKESSLSGGTSPEGEVTKMVVVMVTAFVFCWLPYAAFAMYNVVNPEAQ 0
0 IDYALGAAPAFFAKTATIYNPLIYIGLNRQ 0
0 FRDCVVRMIFNGRNPWVDELVGSQVSSTGSQLTAVSSNKVAPA* 0

>PPINb_cioInt Ciona intestinalis 137 +- 67340 71147 3808 new 61% classifies perhaps as PIN jgi gene model wrong both ends
0 MTTAETTTECYEKNPYIRNEMGWVPKHILIAERHIYTILAVYMTFIFLLAVSLNGFVIIATMKNK 0
0 KLRQPLNYIIINLSIADFLSGLVGGFIGMISNSAGYFYFGKTVCILEGYIVSVA 1
2 GVCGLMSISVMAFERYFVVCKPYGPFTLTNTHAAL 1
2 GIGFTWTWSVLWSTPGLIWLDGYVPEGLGTSCAPNWFSKNK 2
1 SERIFIFVYFVFCFFIPLLVIIICYGKIVLFLKQVSLY 0
0 ATRQSSASSNRQADNKVTKMVLVMISAFLICWTPYGVLSLYNAINPDKQ 0
0 LDYGLGAVPVFFAKTANIYNPLIYIGLNKQ 0
0 FRDGVIKMVFRGRNPWAEEMSTQQRQRSTEAGQPIVSNEV* 0

>PARIE_utaSta Uta stansburiana lizard ancestral shift in counterion gusducin and Go
0 MENDSSLATELAEGAIVKPTIFPKAGYGVLAFLMFLNALFSIFNNSLVIAVTLKNPQLRNPINIFILNLSFSDLMMSLCGTTIVIATNYYGYFYLGRKFCIFQGFAVNYF 1
2 GIVSLWSLTILAYERYNVVCQPLGTLQMSTKRGYQLLGFIWVFCLFWAVVPLFGWSSYGPEGVQTSCSIGWEERSWSNYSYLIVYFLSCFFIPVLIIGFSYGNVIRSLHG 0
0 LNKKVEQLGGKSSPEEEFRAVIMVLVMVVAFLICWLPYTVFALIVVFNPALNISPLAATIPTYLSKTSPVYNPIIYIFLNKQ 0
0 FRDCAVEFITCGQVVLTSPEEDISTSAIPVEGKGPCKINQVTPV* 0

>PARIE_anoCar Anole carolinensis KERA DCN BTG1 PARIE EEA1 NUDT4
0 MENESSLVLEGAEGYIVRPTIFPRAGYGVLAFLMFINALFSLFNNFLVIAVTLKNPQLRNPINIFILNLSFSDLMMSICGTTIVIATNYHGYFYLGRRFCIFQGFAVNYF 1
2 GIVSLWSLTILAYERYNVVCQPLGTLQMSTQRAYQLLGFIWVFCLFWAVVPLFGWSSYGPEGVQTSCSIGWEERSWNNYSYLIVYFLSCFFIPVLIIGFSYGNVIRSLHG 0
0 LNKKVEQLGGKSNPEEEFRAVIMVLVMVVAFLICWLPYTLFALTVVFNPALNISPLAATIPTYLSKTSPVYNPIIYIFLNKE 0
0 FRECAVEFITCGKVVLTSPEEDISTSAISDEGIAPCKINQVTPV* 0

>PARIE_xenTro Xenopus tropicalis parietopsin
0 MDGNSTTPGIAVNLTVMPTIFPRSGYSILSFLMFLNAVFSICNNAIVILVTLKHPQLRNPINIFILNLSFSDLMMALCGTTIVVSTNYHGYFYLGKQFCIFQGFAVNYF 1
2 GIVSLWSLTLLAYERYNVVCEPIGALKLSTKRGYQGLVFIWLFCLFWAIAPLFGWSSYGPEGVQTSCSIGWEERSWSNYSYIISYFLTCFIIPVGIIGFSYGSILRSLHQ 0
0 LNRKIEQQGGKTNPREEKRVVIMVLFMVLAFLICWLPYTVFALIVVINPQLYISPLAATLPTYFAKTSPVYNPIIYIFLNKQ 0
0 FRTYAVQCLTCGHINLDSLEEDTESVSAQAENMLTPKTNQVAPA* 0

>PARIE_takRub Takifugu rubripes (teleost)
0 MDSNSTPWSSPPAPLQAEAVTVAPTIFPRVGYSILSFLMFINTVLSVFNNSLAIAVMLKNPSLLQPINIFILSLAVSDLMIGLCGSLVVTITNYHGSFFIGHTACVFQGFAVNYF 1
2 GLVSLCTLTLLAYERYNVVCKPRAGLKLTMRRSIIGLLFVWTFCLFWAVTPLLGWSSYGPEGVQTSCSLAWEERSWNNYSYLILYTLLCFIFPVGVIIYCYCKVLTSMNK 0
0 LNKSVELQGGLSCRRENKHAINMVLAMIIAFFVCWLPYTALSVVVVVDPELHIPPLVATMPMYFAKTSPVYNPIIYFLSNKQ 0
0 FRDATLEVLSCSRYIPHASSRVSINMRSLNRRSVNTHSKVSPL* 0

>PARIE_gasAcu Gasterosteus aculeatus (stickleback)
0 MDSNSTLWSSGSPPPSIHGKMLTITPTIFPRVGYSILSFLMFINTVLTVFNNVLVITVLVRNPSLLQPMNVFILSLAVSDLMIGLCGSLVVTITNYHGSFFIGHTACIFQGFAVNYF 1
2 GLVSLCTLTLLSYERYNVVCRPRNALKLSMRRSIHGLLIVWTFCLFWAVAPLFGWSGYGPEGVQTSCSLAWEERSWSNYSYLVLYTLLCFIVPVAVIIYCYAKVLTSMNT 0
0 LNRSVEVQGGRSSQKENDHAVSMVLAMIIAFFSCWLPYTALSVVVVVDPTLYIPPLVATMPMYFAKTSPVYNPIIYFLSNKQ 0
0 FRDAALEMLSCGRYIAHMPNTVSINMRSLNRRSRLSSLSRNVNSHSKVLPL* 0

>PARIE_danRer Danio rerio 
0 MENFAKTELTMMVQPTIFPRVGYSILSYLMFINTTLSVFNNVLVIAVMVKNLHFLNAMTVIIFSLAVSDLLIATCGSAIVTVTNYEGSFFLGDAFCVFQGFAVNYF 1
2 GLVSLCTLTLLAYERYNVVCKPMAGFKLNVGRSCQGLLLVWLYCLFWAVAPLLGWSSYGPEGVQTSCSLGWEERSWRNYSYLILYTLMCFILPTVIITYCYSNVLLTMRK 0
0 INKSIECQGGKNCAEDNEHAVRMVLAMIIAFFICWLPYTAISVLVVVNPEISIPPLIATMPMYFAKTSPVYNPIIYFLTNKR 0
0 FRESSLEVLSCGRYISRETGGPLMGSSMQRGQSRVNPV* 0

>ENCEPH_homSap encephalopsin OPN3 panopsin encephalopsin 1q43 - 47250 4 chr1:239,823,075-239,870,324 402 cone opsin with intron loss
0 MYSGNRSGGHGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_monDom encephalopsin Monodelphis domestica 82% funny business with extra intron, alt splicing
0 MYSDNSSDDGGGGYWGSGRAGGASGTGVTGEPGPEGSPRQAPLFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 1
2 GIVSIMTLTVLAYERYNRIVHAKVINFSWAWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVIFLFFGCLMLPVGVMAYCYGHILYAIRM
0 LRCVEELQTIQVIKILRYEKKVAKMCFLMIAIFLFCWMPYAVICLLVANGYGSLVTPTVAIIASLFAKSSTAYNPIIYIFMSRK 0
0 FRRCLLQLLCFRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDENDKNSGTKVNVIQVRPL* 0

>ENCEPH_galGal chicken encephalopsin
0 MHSGNGTGATSRPQLAAAGHEVPGERPLFSAGTYELLALLIATIGTLGVCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVCGVSLTFMSCLRSRWVWDAAGCVWDGFSNSLF 1
2 GIVSIMTLTVLAYERYIRVVHAKVIDFSWSWRAITYIWLYSLAWTGAPLLGWNRYTLEIHGLGCSMDWKSKDPNDTSFVLLFFLGCLVAPVVIMAYCYGHILYAVRM 0
0 LRCVEDFQTSQVIKLLKYEKKVAKMCFLMISTFLICWMPYAVVSLLVTYGYSNLVTPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRQCLLQLLCFRLMRFQRIMKEPSGAGNVKPIRPIVMSQKVGDRPKKKVTFSSSSIIFIIASDDTQQIDDNSKHNGTKVNVIQVKPL* 0

>ENCEPH_anoCar lizard encephalopsin
0 MFSANGTRSGAGSDLEPGPGQQQQQREASEEEERGAGLSPFSAGTYELLALLVAAIGLLGLCNNLLVLVLYAKFKRLRTPTHLFLVNISLSDLLVSLFGVSFTFGSCLRHRWVWDAAGCVWDGFSNSLF 1
2 GIVSIMTLTVLAYERYIRVVHARVIDFSWSWRAITYIWLYSLAWTGAPLLGWNHYTLEIHGLGCSVDWQSKEPSDSSFVLFFFLGCLAAPVGIMAYCYGHILHAIRM 0
0 LRCVEDLQSIQVIKILRYEKKVAKMCFLMVTTFLICWMPYAVVSLLIAYGYGHLITPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRRCLVQLFCVQFLRFKRTLKEQPAIESNKPIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDDTEQIDVSTKCSDTKINVIQVKPL* 0

>ENCEPH_xenTro Xenopus frog encephalopsin called teleost multiple tissue TMT opsin in fish
0 MPVTNGSHNNSISWLHSKDMFTEDTYHFLALIVATVGFLGLVNNLLVLILYCKFKRLQTPTNLLFFNTSLCHFVFSLLAITFTFMSCVRGSWAFSVEMCVFHGFSKNLL 1
2 GIVSFGTLTVVAYERYARVVYGKYVNSSWSKRSITFVWVYSLAWTGFPLIGWNLYTFETHKLDCSFEWTATDPKDTAFVLLFFLACITLPLSIMAYCYGYILYEIQK 0
0 LRSVKNIQNFQEITILDYEIKMAKMCLLMMLTFLIGWMPYTILSLLVTSGYSKFITPTITVMPSLLAIASAAYNPVIHIFTIKK 0
0 FRQCLVQLLPPINFHPPINPPINNFWRLLKNLNGRLAMKKVKPVLGKGRSHNRPEKKVPPINFSSSDFFTRTTSDTGTHGITESTKGKRTNVRLIQVHPL* 0

>ENCEPH4a_takRub Takifugu rubripes length=403 AF402774 multiple tissue opsin organs and cell lines exhibit circadian oscillations in clock gene 
0 MIVSNVSLSGCAGVNGAVCAAEGHQAGGSDRSTLTPTGNLVVSVFLGFIGTFGLVNNLLVLVLFCRYKMLRSPINLLLMNISISDLLVCVLGTPFSFAASTQGRWLIGEAGCVWYGFANSLF 1
2 GVVSLISLAVLSFERYSTMMTPTEADPSNYCKVCLGITLSWVYSLVWTVPPLFGWSSYGPEGPGTTCSVNWTAKTTNSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQ 0
0 VSGINASTSRKREQRVLCMVVIMVICYLLCWLPYGVVALLATFGPPDLVTPEASIIPSVLAKSSTVINPIIYVFMNKQ 0
0 FYRCFLALLCCQDPRSGSSMKSSSKVATKAKGVTPTGQRRTDFLYMVASLGRPAATIPQLGPSFDATNDFTKPPSSDTIKPVVVSLAAHCDG*

>ENCEPH4b_takRub Takifugu rubripes length=342 64% +CES1 +ENC
0 MIVCNVSLSCAHCPGEGTAANDAYAQASGSLATPTLSQRGHLVVAVCLGFIGTVGFLSNFLVLALFCRYRALRTPMNLMLVSISASDLLVSVLGTPFSFAASTQGRWLIGRAGCVWYGFVNACL 1
2 GIVSLISLAVLSYERYCTMVSSTIASNRDYRPVLGGICFSWFYSLAWTVPPLLGWSRYGPEGPGTTCSVDWRTQTPNNISYIVCLFTFCLLLPFFVILYSYGKLLHTIRQ 0 
0 VRRVSSTVTRRREHRVLVMVVAMVVCYLICWLPYGVTALLATFGPPNLLTPEATITPSLLAKFSTVINPFIYIFMNKQ 0
0 FYRCFRAFLNCSTPKRDSTVRTFTRISLRALRQDQQQKGSALAPSSARPTPNSIHESSLKGSHSTPSNGGAAAAKSPAANRSKPKLILVAHYRE* 0

>ENCEPH_takRub Takifugu rubripes encephalopsin syntenic to mammal
0 MNPANGSRSERSAEQLLFSGDTYRVLAFTIGTIGAFGFCNNFVVLALYCRFKRLRTPTNLLLVNISLSDLLVSLFGINFTFAACVQGRWTWTQATCVWDGFSNSLF 1
2 GIVSIMTLAALAYERYIRVVHAQVVDFPWAWRAIGHIWLYALAWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVQM 0
0 IRSIQDLQTVQIIKILRYEKKVSVMFFLMISCFLLCWTPYAVVSMMVAFGRRSMVSPTMAIIPSFFAKSSTAYNPLIYVFMSRK 0
0 FRHCLLQLLCSRLSWLQRSLKERPLAPVQRPIRPIVMSRPCGKGNRPKKKVTFSSSSIVFIITSDDFGQLDVTSKSGDSADVNAIQVRPL* 0

>ENCEPH_tetNig encephalopsin
0 MSSADDSRSARSGEPSLFAVHTYRLLAAAIGAIGVLGFCNNLAVAALYWRFRRLRTPTNLLLLNISLSDLLVSLLGVNFTFAACVQGRWTWNQATCVWDGFSNSLF 1
2 GIVSIMTLAALAYERYIRVVHAQVVDFPWAWRAIGHIWLYSLAWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVHM 0
0 IRSIQDLQTVQIIKILRYEKKVSVMFFLMISCFLLCWTPYAVVSMMVAFGRKSMVSPTVAIIPSFFAKSSTAYNPVIYVFMSRK 0
0 FRRCLLQLLCSRLSWLQRGLKERPLAPVQRPIRPIVVSRPCGKGTRPKKKVTFSSSSIVFIITSDDFRQLDVTSRAGDSADVNAIQVRPL* 0

>ENCEPH_gasAcu Gasterosteus aculeatus (stickleback) encephalopsin
0 MNPDNGTREERSTDHSIFAVGTYKLLAFAIGTIGVFGFCNNVVVIVLYCKFKRLRTPTNLLVVNISLSDLLVSVIGINFTFVSCIRGGWTWSRATCIWDGFSNSLF 1
2 GIVSIMTLASLAYERYIRVVHAQVVDFPWAWRAIGHIWLYSLVWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVQM 0
0 LRSIQDLQTVQIIKILRYEKKVAVMFLLMISCFLLCWTPYAVVSMMEAFGRKNMVSPTVAIIPSFFAKSSTAYNPLICVFMSRK 0
0 FRRCLMQLLCSRVTCLQCNLKERPLAPVQRPIRPIVVSAACGGGRVRPKKRVTFSSSSIVFIITRNDIRHTDVTSNTRESSEANVFQVRPL* 0

>ENCEPH4_braFlo Branchiostoma floridae Amphiop4 AB050608 Un - 207841137 207851157 10021 new exon12 and 34 + perfect fit +CES1 -ENC -RTF1
0 MALYNNTSSPSQDLLWDAPYSQGHIWDNSSASNSSEDVMDQGKVELQDFSDAGYTAIATCLALI 1
2 GFVGFTNNFVVILLIGCHRQLRTPFNLLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANSLF 1
2 GIVSLVTLSALAFERYCVVVRSSDMLTYKSSLVVITFIWLYSLLWTSLPLLGWSSYQFEGHN 0
0 VGCSVNWVQHNPDNVSYIVTLMVTCFFVPMVVVCWSYAWIWRTVRM 0
0 SSEAKPECGNSQNAGRLVTTMVVVMIICFLVCWTPYAVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ 0
0 FREFLLARLQRVCCRQQAVPRVTPMDDNVHVRLGGEGPSQSQQFLPAGENVENVDMLEYVQENCKPKADSLSTISE* 0

>ENCEPH4_braBel Branchiostoma belcheri Amphiop4 pinopsin encephalopsin introns from braFlo 83%
0 MPLYNTSSGPTQGLPWDTPYSQDPIWNDSSPSNSSEDAVVDQGRGELQDFSDAGYTAIATGLALI 1
2 GLVGSMNNFVVILLIGCHRQLRTPFNLLLLNVSVADLLVSVCGNTLSFASAVQHRWLWGRPGCVWYGFANSLF 1
2 GIVSLVTLSALAFERYCVVVRSSEMLTYKSSLGMIAFIWMYSLLWTSLPLLGWSSYQFEGHS 0
0 VGCSVNWVKHNVNNVSYIITLMVTCFFVPMVVVCWSYACIWRTVRM 0
0 SAEMKSEFGNPQNTGRLVTTMVVVMIVCFLVCWTPYTVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ 0
0 FREFLLARLRTFCCRQPRMLRVTPMDDNAHARLVGEGPSHAQQVIPSEENGENVEMRKVQGNQLKADSLSTISE* 0

>ENCEPH5_braBel Branchiostoma belcheri Amphiop5 AB050609 early dup of ENCEPH extra Nfrag in mrna
0 MLGIYNVVNATEYGNNTTFAAWDFKRNGTGGEEEVEFFGYDAVAGVIAIIGVVGFVSNGAVVVLFLKFPQLRTPFNLLLLNMAVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 1
2 GLVSLISLAVISFLRYRMVVKPKGPGSSYLTYTKVGLAILFIYLYCLLWTTLPIAGWSSYQLE 0
0 GPKIGCSVAWEEHSWSNTSYIVVLFITCLFAPLLIIVYSYYRLWHKVKQ 0
0 GSRNLPAAMRKSSQKEQKIAMMVIVMITCFMVCWLPYGAMALVVTFGGERLISHTAAVVPSLLAKSSTCYNPVVYFAMNSQ 0
0 FRRYFQDLLCCGRRLFDVSQSVVTGNTAMPRNNSQGFRKDDSDQKQDNGLPKQSEGPMCDHSSNESQMEGSRHNTAASQQWIEMQTIAVVVKAVEVDTSAANEP* 0

>ENCEPH5_braFlo Branchiostoma floridae extra 00 intron chrUn:398,023,923-398,103,839 +ETF1 -ENC -RTF1
0 MLGMHNVMNATDYDNNNATFAAWNFQRNGTTEEEVEFSGFDTVAVVIAAIGIAGFLSNGAVVLLFLKFRQLRTPFNMLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 1
2 GLVSLISLAVISYERYRMVVKPKGPGSSYLTYNKVGLAIIFIYLYCLLWTTLPIVGWSSYQLE 0
0 GPKISCSVAWEEHSLSNTSYIVAIFIMCLLLPLLIIIYSYCRLWYKVKK 0
0 GSQNLPPAIRKSSQKEQKIARMVVVMITCFLVCWLPYGAMALVVSFGGESLISPTAAVVPSLLAKSSTCYNPLVYFAMNNQ 0
0 FRRYFQDLLCCGRRLFDASASVNTCNTSAMPRHSPVFQKPDSDQYNGIQKSREPQMRTTGQNAPYRQWIEMQTIAVVVKADEVNNKFGEVKT* 0

>ENCEPH_apiMel Apis mellifera (honey bee) NM_001039968 328 aa ciliary opsin Gt pteropsin clock -ENC -PSMA3
0 MSLNRSTMEHVIYEDQVSPVMYIGAAIALGFIGFFGFTANLLVAIVIVKDAQILWTPVNVILFNLV 0
0 FGDFLVSIFGNPVAMVSAATGGWYWGYKMCLW 2
1 YAWFMSTLGFASIGNLTVMAVERWLLVARPMQALSIR 2
1 HAVILASFVWIYALSLSLPPLFGWGSYGPEAGNVSCSVSWEVHDPVTNSDTYIGFLFVLGLIVPVFTIVSSYAAIVLTLKKVRKRA 1
2 GASGRREAKITKMVALMITAFLLAWSPYAALAIAAQYFN 0
0 AKPSATVAVLPALLAKSSICYNPIIYAGLNNQFSRFLKKIFDARGSRTAVPDSQHTALTALNRQEQRK* 0

>ENCEPH1_anoGam Anopheles gambiae XM_312503 GPROP11 adjacent head-to-head tandem GPROP12
0 MYDVTDAAAINSDHQELMAPWAYNGAAVTLFFIGFFGFFLNIFVIALMYKDVQ 0
0 LWTPMNIILFNLVCSDFSVSIIGNPLTLTSAISHRWLYGKSICVAYGFFMSLL 1
2 GIASITTLTVLSYERFCLISRPFAAQNRSKQGACLAVLFIWSYSFALTSPPLFGWGAYVNEAANI 1
2 SCSVNWESQTANATSYIIFLFIFGLILPLAVIIYSYINIVLEMRK 0
0 NSARVGRVNRAERRVTSMVAVMIVAFMVAWTPYAIFALIEQFGPPELIGPGLAVLPALVAKSSICYNPIIYVGMNTQ FRAAFWRIRRSNGVAGQPDSNNTNNSNRDKESARHTAKEGL
ECSLDFCHWTVRGTRVSISSAERNVPAPAARERSGGHSVTGSREESRDRHVTLKTMLSVGPRSPSSVAPVAADCSTTDVPTSGDGSVRIVRQDSELSVIHDGGGGGGGSSSRVLVIKSQKPRSNML* 0

>ENCEPH2_anoGam Anopheles gambiae XM_312502 GPROP12
0 MNDAPNDVAASAVDYEDLMAPWAYNASAVTLFFIGFFGFFLNLFVIALMCKDMQ 0
0 LWTPMNIILFNLVCSDFSVSIIGNPLTLTSAISHRWIFGRTLCVAYGFFMSLL 1
2 GITSITTLTVLSYERYCLISRPFSSRNLTRRGAFLAIFFIWGYSFALTSPPLFGWGAYVQEAANI 1
2 SCSVNWESQTKNATTYIIFLFVFGLVVPLIVIVYSYTNIIVNMRE 0
0 NSARVGRINRAEQRVTSMVAVMIVAFMVAWTPYAIFALIEQFGPPELIGPGLAVLPALVAKSSICYNPIIYVGMNTQ FRAAFSRVRNKGQQAAADQNTTTMQRELTKSSRDMVECSF
DFCRKKSRFKISLVKPTAPLAVVDVSSTSHRDKGTSRSPLDQTVLNETNEDVGRERSGGGGGGGAYAGTRFVRPDFELSVINSGKSILIKSKNFRSNLL* 0

>CILL2_plaDum Platynereis dumerilii CT030681 htgs 171779 bp new CILL1 ENCEPH PARIE 44% e-65 393 5 exons 1 missing
0 MDDLGFLGNSSVNYTVPLLQEDPLLLRILYFGPTSYVITAIYLCIVGVIGTLSNGVIMYLYFKDKSLRSPMNLLFVNLAMSDFTVAFFGAMFQFGLTCTRKYMSPGMALCDFYGFITFLG 1
2 GLASEMNLFIISVERYLAVVRPFDVGNLTNRRVIAGG 1
2 VFVWLYSLVFAGGPLVGWSSYRPEGLGTWCSISWQDRSMNTMSYVTAVFLGCYFFPVSIIIFCYFNVWRKVKE 0
0 AADAQGAGTAGKAEKSIFRMSVIMVTCYLTAWTPYAIVCLIASYGPPNGLPIYAEVLPSLFAKSSQVYNPIIYVLMNKP 0
0 0* 0

>CILL1_plaDum Platynereis dumerilii AAV63834 Gt lophotrochozoa ciliary opsin mRNA polychaeta unavailable genomically
0 MDGENLTIPNPVTELMDTPINSTYFQNLNAETDGGNHYIYNAFTATDYNICAAYLFFIACLGVSLNVLVLVLFIKDRKLRSPNNFLYVSLALGDLLVAVFGTAFKFIITARKTLLREEDGFCKWYGFITYLG 1
2 GLAALMTLSVIAFVRCLAVLRLGSFTGLTTRMGVAAMA 1
2 FIWIYSLAFTLAPLLGWNHYIPEGLATWCSIDWLSDETSDKSYVFAIFIFCFLVPVLIIVVSYGLIYDKVRK 0
0 VAKTGGSVAKAEREVLRMTLLMVSLFMLAWSPYAVICMLASFGPKDLLHPVATVIPAMFAKSSTMYNPLIYVFMNKQ 0
0 FRRSLKVLLGMGVEDLNSESERATGGTATNQVAAT*

>RGR_homSap 10q23.1 + 14136 7 chr10:85,994,789-86,008,924 295 exons distinct retinal pigment epithelium and Mueller cells
0 MAETSALPTGFGELEVLAVGMVLLVE 1
2 ALSGLSLNTLTIFSFCKTPELRTPCHLLVLSLALADSGISLNALVAATSSLLR 2
1 VSHRRWPYGSDGCQAHGFQGFVTALASICSSAAIAWGRYHHYCT 1
2 RSQLAWNSAVSLVLFVWLSSAFWAALPLLGWGHYDYEPLGTCCTLDYSKGDR 2
1 NFTSFLFTMSFFNFAMPLFITITSYSLMEQKLGKSGHLQ 0
0 VNTTLPARTLLLGWGPYAILYLYAVIADVTSISPKLQM 0
0 VPALIAKMVPTINAINYALGNEMVCRGIWQCLSPQKREKDRTK* 0

>PER_homSap peropsin RRH 4q25 7 chr4:110,968,599-110,985,310 337 + 16712 retinal photoisomerase Retinal pigment epithelium 
0 MLRNNLGNSSDSKNEDGSVFSQTEHNIVATYLIMA 1
2 GMISIISNIIVLGIFIKYKELRTPTNAIIINLAVTDIGVSSIGYPMSAASDLYGSWKFGYAGCQ 0
0 VYAGLNIFFGMASIGLLTVVAVDRYLTICLPDV 1
2 GRRMTTNTYIGLILGAWINGLFWALMPIIGWASYAPDPTGATCTINWRKNDR 2
1 SFVSYTMTVIAINFIVPLTVMFYCYYHVTLSIKHHTTSDCTESLNRDWSDQIDVTK 0
0 MSVIMICMFLVAWSPYSIVCLWASFGDPKKIPPPMAIIAPLFAKSSTFYNPCIYVVANKK 2
1 FRRAMLAMFKCQTHQTMPVTSILPMDVSQNPLASGRI* 0

>PERa_braBel Branchiostoma belcheri Amphiop3 peropsin AB050610
MDIPTETPYGAEEDIGESAGWRWTETDKNGFHKYDHLIVGLYLFVIGIIGTIENGITLATFSKFRSLRSPTTMLLVHLAI
ADLGICIFGYPFSGASSLRSHWLFGGVGCQWYGFNGMFFGMANIGLLTCVAVDRYLVICRHDLVDKVNYNTYGVMAALGW
LFAAFWAALPLVGWAEYALEPSGTACTINFQKNDSLYISYVTSCFVLGFVVPLAVMAFCYWQASCFVSKVLKGDIAGDLT
FPVAANVDWEYQNHFSKMCLAMVAAFVVAWTPYSVLFLFAAFWNPADIPAWLTLLPPLIAKSSALYNPIIYIIANRR FRNAICSMMKGQDPDVEDDEHADEHRVRSIEDNDKEIISMVNLNMTV*

>PERb_braBel Branchiostoma belcheri Amphiop2 peropsin RRH AB050607
MIPTNNNTENNDLEWGLEKEHGVSATIMGVYLTIVGLVATVGNATVVLMFIMKWRQLCRKAPNLLVINLAAANLCITIFG
YPFSASSGYAHQWLFPDAICTLYGFSCFLLSMVSMHTLCLISAHRYITICRPEHASKLTMNRTVLAVIGTWLYAIAVAVP
PLFNIARYTYEPSGLSCTIDFRVTTVADLVYLGSLIVLCYVIHVAVMATCYFKIIRKFSRHRFRQVRDIRTSHQRSFEMG
VTMRCILMTLFYLLSWTPYTAVCIWTMVGPPPPVVVSMAAALIAKTHCAFNPILYAFMSEVYRKLVFRTMCPCCFNRISC
KFVGTPTGGSKVSANPDIFTVDYNSRDQAVQINKAPSRRFCFVMETSEDLGSDDTGLTGHSGLWRSGAEVEGLGGLQVTQ
SPSVSGSELSLSLLDFLPPKPSGRAVSAKLPSPPALNSERATCPESSQQPSDRPATGLRQYQKGDTTRSSVGDLILTEDD
VTNLPPASETWGRKKSENPLSYRQTTRRTFGRSRKHSYIVD*

>PERc_braBel Branchiostoma belcheri Amphiop1 peropsin RRH AB050606 Go 
MNASPSSWLSSGEFFTDSPENSSEWPWTDGPTDTTWRHHQSVDSVSYEGYLASAIYITLTGLIAFFGNVITITVFLTEKE
FRKKQQNGFVLNLAIADLSVCVFAYPSSAIAGYAGRWVLGDVGCTIYGFLCFTFALVSMVTLCVISIYRYILICKPQYAH
LLTHRRTVYVIIGTWLYALVFTVPPLVGVKRYTYEPMQITCSLDWNVQHPGEKAYIAAVLVIVYVLQVLIMCFCYFNIIF
KSANLKFAALASEKTKMAAKKDTWKTSVMCLTMVVSFLIAWTPYAVSSTWDILSAEDLPIIATILPSLFAKSSCMMNPII
YACCNTK FRQAAVKSFRKLCGMCKQKVPLSTPQVVLAMQRNTEFTSTVEPTGQAFPMRVLPSISATHTAL*

>NEUR_homSap neuropsin 6p12.3 chr6:47,857,757-47,902,075 7 354
0 MALNHTALPQDERLPHYLRDGDPFASKLSWEADLVAGFYLTII 1
2 GILSTFGNGYVLYMSSRRKKKLRPAEIMTINLAVCDLGIS 1
2 VVGKPFTIISCFCHRWVFGWIGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICYLSY 1
2 GVWLKRKHAYICLAAIWAYASFWTTMPLVGLGDYVPEPFGTSCTLDWWLAQASVGGQVFILNILFFCLLLPTAVIVFSYVKIIAKVKSSSKEVAHFDSRIHSSHVLEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGRPDSIPIQLSVVPTLLAKSAAMYNPIIYQVIDYK FACCQTGGLKATKKKSLEGFR 2
1 LHTVTTVRKSSAVLEIHEE 0
0 WE* 0

>MEL1_homSap melanopsin rhabdomeric OPN4 10q23.2 + 11903 10 chr10 GLUD1 MMRN2 BMPR1A LDB3 OPN4 WAPAL GRID1
0 MNPPSGPRVPPSPTQEPSCMATPAPPSWWDSSQSSISSLGRLPSISPT 0 
0 APGTWAAAWVPLPTVDVPDHAHYTLGTVILLVGLTGMLGNLTVIYTFCR 2
1 SRSLRTPANMFIINLAVSDFLMSFTQAPVFFTSSLYKQWLFGET 1
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATFGVASKRRAAFVLLGVWLYALAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYMSFTPAVRAYTMLLCCFVFFLPLLIIIYCYIFIFRAIRETGR 2
1 ALQTFGACKGNGESLWQRQRLQSECKMAKIMLLVILLFVLSWAPYSAVALVAFAG 2
1 YAHVLTPYMSSVPAVIAKASAIHNPIIYAITHPKYR 2
1 VAIAQHLPCLGVLLGVSRRHSRPYPSYRSTHRSTLTSHTSNLSWISIRRRQESLGSESEV 0
0 GWTHMEAAAVWGAAQQANGRSLYGQGLEDLEAKAPPRPQGHEAETPGK 0
0 TKGLIPSQDPRM* 0

>MEL1_monDom Monodelphis domestica (opossum) BMPR1A LDB3 OPN4 WAPAL GRID1
0 MNPSPMLRGLSCPAQDTNCTKIMASMSEWNNTEEDAYHLVDLPSIAPT 0
0 AVVLPPSSQNIFPTADVPDHAHYTIGATILAVGFTGVLGNLLVIYTFCR 2
1 LRTPANMFIINLAISDFFMSFTQAPVFFASSMYKRWIFGEK 1
2 ACEFYAFCGALFGITSMITLMAIALDRYFVITRPLASIGVISKKKTGFILLGVWLYSLAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYTTFTPSVRAYTMLLFCFVFFIPLIVIIYCYIFIFRAIQDTNK 2
1 AVHSIGSGESTASPRHCQRMKNEWKMAKIALVVILLYVLSWAPYSTVALVAFAG 2
1 YSHILTPYMNSVPAIIAKASAIHNPIIYAISHPKYR 2
1 MAIAQNFPCLRALLCVRHPRTRSFSSYRFTRRSTMTSQASDISWLPRGRRQLSLGSESEI 0
0 GWNNMEAGTTSLTSRNQQGSCRMDQETMETRELAAIAKAKGRSWETLEK 0
0 TLEEMDDSSLLEVSVDMEQ* 0

>MEL1_galGal OPN4 melanopsin1 BMPR1A LDB3 OPN4 WAPAL GRID1
0 MDLPPRAPT 0
0 KMTVKDVRGAFPTVDVPDHAHYTIGTVILIVGITGTLGNFLVIYAFCR 2
1 SRTLQKPANIFIINLAVSDFLMSITQSPVFFTNSLHKRWIFGEK 1
2 GCELYAFCGALFGITSMITLMVIALDRYFVITKPLASVRVMSKKKALIILVGVWLYSLAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYMTFTPSVRAYTMLLFCFVFFIPLIAIIYSYVFIFEAIKKANK 2
1 SVQTFGCKHGNRELQKQYHRMKNEWKLAKIALIVILLYVISWSPYSVVALVAFAG 2
1 YSHVLTPFMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 TAIATYVPCLGFLLRVSPKESRSFSSYPSSRRTTITSQSSETSGLQKGKRRLSSISDSES 0
0 GCTDTETDITSMISRPASSQVSYEMGEDTTQTSDLGGKPKVKSHDSGIFRK 0
0 TVVDADEIPMVEINDTEHSATSTCKTSEKCNVEEIQ 0
0 RSESLSGIGLREGESRHRTSASQIPSIIITYSNVQGVELHSGYSAGFLHPKNKSHKQNKSSNS* 0

>MEL1_xenTro Xenopus tropicalis melanopsin  
0 MNYQSVRKGITCPPQDANCSRILESLNSWNNSEVNSYKLVELPPIVTT 0
0 ETPQYEIHHVYPTVDVPDHVHYVVGAVILAVGITGMLGNFLVIYAFCR 2
1 SRSLRSPANMFIINLAITDFLMSVTQAPVFFATSLHKRWIFGEK 1
2 GCELYAFCGALFGITSMITLMVIAVDRYFVITRPLTSIGVMSKKRAVLILSGVWLYSLAWSLPPFFGW 1
2 SAYVPEGLLTSCTWDYMTFTPSVRAYTMLLFCFVFFIPLFIIIYCYIFIFKAIKNTNR 2
1 AVQKIGTDNNKESHKQYQKMKNEWKMAKIALIVILLYVVSWSPYSTVALLAFAG 2
1 YASILTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 MAIAKYIPCLGSLLRVKRRDSRSYSSYPSSRRSTVTSHCSQSSDVGGHPKLKNHLPSVSDSES 0
0 GWTDTEADSSVNSRPASRQVSYEMGKDTTETNDLKSKAKLKSHDSGIFEK 0
0 TSMDADDISLVELGTVDRSSPIM 0
0 ANKHLNGLGQRKGDSFTRRSPSSRIPSIVVTHSNHQGSPAAVRHNSTLPGIKVSNSQDREKELKRQIEKVKQYVPIVTITSDTENSTGGFSNELLPANTS* 0

>MEL1_danRer Danio rerio (zebrafish) Gq XM_695228 +BMPR1A +LDB3 OPN4 +USP54 +CAMK2G  11 exons  AY882945 opn4d
0 MMSGAAHSVRKGISCPTQDPNCTRIVESLSAWNDSVMSAYRLVDLPPTTTTTTSVA 0
0 MVEESVYPFPTVDVPDHAHYTIGAVILTVGITGMLGNFLVIYAFSR 2
1 SRTLRTPANLFIINLAITDFLMCATQAPIFFTTSMHKRWIFGEK 1
2 GCELYAFCGALFGICSMITLMVIAVDRYFVITRPLASIGVLSQKRALLILLVAWVYSLGWSLPPFFGW 1
2 SAYVPEGLLTSCTWDYMTFTPSVRAYTMLLFIFVFFIPLIVIIYCYFFIFRSIRTTNE 2
1 AVGKINGDNKRDSMKRFQRLKNEWKMAKIALIVILMYVISWSPYSTVALTAFAG 2
1 YSDFLTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 LAIAKYIPCLRLLLCVPKRDLHSFHSSLMSTRRSTVTSQSSDMSGRFRRTSTGKSRLSSASDSES 0
0 GWTDTEADLSSMSSRPASRQVSCDISKDTAEMPDFKPCNSSSFKSKLKSHDSGIFEK 0
0 SSSDVDDVSVAGIIQPDRTLTN 0
0 AGDITDVPISRGAIGRIPSIVITSESSSLLPSVRPTYRISRSNVSTVGTNPARRDSRGGVQQGAAHLSNAAETPESGHIDNHRPQYL* 0

>MEL1d_danRer Danio rerio (zebrafish) frag Gq XM_695228 +BMPR1A +LDB3 OPN4 +USP54 +CAMK2G diff chrom, WGDup
0 QVAMVQDVRHPFPTVDVPDHAHYTIGSVILAVGITGMVGNLLVMYAFCK 2
1 SRSLRTPANMFIINLAVTDFLMCVTQTPIFFTTSLHKRWIFGEK 1
2 GCELYAFCGALFGICSMITLMIIAVDRYFVITRPLASIGVMSRKRALLILSAAWAYSMGWSLPPFFGW 1
2 SGAYVPEGLLTSCSWDYMTFSPSVRAYTMLLFTFVFFIPLFVIIYCYFFIFKAIRETNR 2
1 AVGKINGEGGPRDSIKKIHRMKNEWKMAKIALIVILLYVISWSPYSCVALTAF 2
1 YADMLTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 SAIAKYIPCLGVLLCVPRRDRFSSSSFISTRRSTLTSQSSETSSNLHRAGKARLSSVSDSES 0
0 GWTDTEADLSTASSRPASRQVSSEIRKDLCDIKHSSSLRLKVKSRDSGIFDR 0
0 0
0 QNDVSEKADEKRPLVRIPSIIVTSETCPAVLPAGHSSRLIPGAPAVTDS* 0

>MEL1_takRub Takifugu rubripes (teleost)
0 MNFGKSALQPPAQQSVVSCGGGGPEPNCTLRLAVTVMMSVRLAELQLHAST 0
0 LQVAMVRPFPTVDVPDHAHYTIGSVILVIGITGMIGNFLVIYAFCR 2
1 SRSLRTPANMFIINLAVTDLLMCVTQTPIFFTTSMYKRWIFGEK 1
2 GCELYAFCGALFGICSMITLTVIAIDRYFVITRPLTSIGVLSRKRAFVILMTVWIYSLGWSLPPFFGW 1
2 SGAYVPEGLLTSCTWDYMTFSPSVRAYTMLLFIFVFFLPLFIIIYCYFFIFRAIRATNK 2
1 AVGKVNGSVHSHSRRRESVKNFQRLQNEWKMAKIALMVILLYVISWSPYSCVALTAFAG 2
1 YADMLTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 LALAKYIPCLGFLLCISPHELQSTSSSFMSLRRSTVTSQTSDISGQFRPQSKPRRSSASDSES 0
0 CLTDTEADLSSMGSRPASRQVSCDISRDTTELPEYKPASSFNSKVKSPDSGIFEK 0
0 TSFDFDASMAASRERSSIPN 0
0 SGEFPEGHVMRRTLARIPSIIITSESSHFLPNGRKASSTTCIANGSDIKVGPR* 0

>MEL1_gasAcu Gasterosteus aculeatus (stickleback)
0 MNAGESELLLPTQQSILPCGDHEPNCPVAQAETLALSAASANGSA 0
0 VQVAMVSRAPHPYPTVDVPDHAHYTIGSVILAIGITGIIGNVLVIYAFSK 2
1 SRSLRTPANMFIINLAITDLLMCVTQAPIFFTTSMHKRWIFGEK 1
2 GCELYAFCGALFGICSMITLTVIALDRYFVITRPLTSIGMMSRRRALLILMGAWTYSLGWSLPPFFGW 1
2 SGAYVPEGLLTSCTWDYMTFTPSVRAYTMLLFIFVFFLPLFIIIYCYFFIFRAIRVTNR 2
1 AVGKMNGSIHSHGSGRDSTKNFHRLQNEWKMAKIALIVILLYVVSWSPYSAVALTAFAG 2
1 YADMLTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 IALAKYIPFLGVLLCVPPRELRSASSSFRSTRRSTVTSQTSDVSSQQRRQGSRNSRLSSASDSES 0
0 CLTDTEADGSSVGSRPASRQVSCDIGRDTAELPEFKPSSSFKSKMKSHDSGIFEK 0
0 SYDTDISMAGVSERGSIPN 0
0 QTDFAEGRDRRSTIGRIPSIVITSETSPFLPTGRNGSCNGRPKTANSSHPGAGSG* 0

>MEL1_oryLat Oryzias latipes (medaka) frag
0 LQVAMVPQTFHPFPTVDVPDHAHYTIGSVILAIGITGIIGNFLVIYAFSR 2
1 SRSLRTPANMFIINLAITDLLMCVTQSPIFFTTSMHKRWIFGEK 1
2 GCELYAFCGALFGICSMITLTVIAIDRYFVITRPLTSIGVLSRKRALLILSAAWAYSLGWSLPPFFGW 1
2 SGAYVPEGLLTSCTWDYMTFTPSVRAYTMLLFIFVFFLPLFIIIYCYVFIFRAIRSTNR 2
1 AVGKINGNTRDAVKSFNRLQNEWKMAKIALIVILLYVISWSPYSTVALTAFAG 2
1 YADMLTPYMNSIPAVIAKASAIHNPIIYAITHPKYR 2
1 MALAKYIPGLGVLLCIHPKDLRSASSSFVSTRRSTVTSQSSDISSQLRRQSTFKSRLSSLSDSES 0
0 GLTDTEADLSSLSSRPASRQVSCEISRDTAELPDFKHTSSFKAKLKNNDSGIFEK 0
0 TSFDTVSIGGVSEHNSIPS 0
0 NRDFGDGNVTRATIGRIPSIVVTSEMSPFLPVGRNGSRTNRSKMANSSAGAGPV* 0

>MEL1_calMil Callorhinchus milii (elephantfish) frag
0 ASVTDAQHHHMFPTVDVPDHAHYIIGATILAVGVTGMVGNFLVIYAFLRYH 2
1 SRSLRTPANTFIINLAATDFLMSVTQSPIFFITSIHKRWIFGEK 1
2 GCELYAFCGALFGITSMITLMVIALDRYFVITRPLASIGVLSHRRAGLIILSLWLYSLAWSLPPFFGW 1
2 SGAYVPEGLLTSCTWDYMTFTPSVRAYTMLLFCFVFFIPLGVIIYCYIFIFRAIKSTNK 2
1 KVGGSTNRESQKQHQRMKNEWKMAKIALIVILLFVISWSPYSTVALTAFAG 2
1 YADMLTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 MAIAKYVPLLGLLLRVSRRDSRTSGQYYSTRRSTLTSQTSDLSGYPRGKGRLSSASDSES 0

>MEL1a_braFlo Branchiostom floridae AmphiMop 12 exons 709aa +chrUn:47589027-47597447 size 8421 +tandem dup assembly error
0 MTELPSFQPPTNSTEEENAVFPTALTEWISE 0
0 VGNQVGEAALKLLSGEGDGMEVTPTPGCTGNASVCNGTDSGGGVVWDIPPLAHYIVGTAVFCVGCCGMFGNAVVVYSFIK 2
1 SKGLRTPANFFIINLALSDFLMNLTNMPIFAVNSAFQRWLLSDF 1
2 ACELYGFAGGLFGCLSINTLMAISMDRYLVITKPFLVMRIVTKQR 0
0 VMFAILLLWIWSLVWALPPLFGWSAYVPEGF 1
2 GTSCTFDYMTPKLSYHIFTYIIFFTMYFIPMGVIIYCYYNIFATVKSGDKQFGKAVKEMAHEDVKNK 0
0 AQQERQRKNEIKTAKIAFIVITLFLSAWTPYAVVSALGTLGYQDLVTPYLQSIPAVFAKSSAVYNPI 1
2 VYAITHPKFRAAVKKHIPCLSGCLPADEEETKTKTRGATTTASMSMTQTTAPTV 0
0 HDPQASVHSGSSVSVDDSSGVSRQDTMMVK 0
0 VEVDNRMEKAGGGAADTAPKDGTSVPTVSAQIEVRPSGNVNTKAEVIPSPQSAAVAHGASASPVPK 0
0 VAELSSSVSLESAAIPGKIPTPLPSQPIAAPIERHMAAMADDPPPKPRGVATTVNVRRSESGYERSQDSLRKK 0
0 AVSETRSRSFNSTKDHFASERQTSTTLNQPRDMYSGDMVKKTRQSPEKQEYDNPAFDAGIAEIDTDSENETEGSYDMLSVRFQAMAEEPPVETYRKASDMSINLGKASLMLTEAHDETVL* 0

>MEL1a_braBel Branchiostoma belcheri (Japanese lancelet) AB205400 Amphi-mop
0 MTEIPSFQPPINATEVEEENAVFPTALTEWFSE 0
0 VGNQVGEVALKLLSGEGDGMEVTPTPGCTGNGSVCNGTDSGGVVWDIPPLAHYIVGTAVFCIGCCGMFGNAVVVYSFIK 2
1 SKGLRTPANFFIINLALSDFLMNLTNMPIFAVNSAFQRWLLSDF 1
2 ACELYGFAGGLFGCLSINTLMAISMDRYLVITKPFLVMRIVTKQR 0
0 VMFAILLLWIWSLVWALPPLFGWSAYVSEGF 1
2 GTSCTFDYMTPKLSYHIFTYIIFFTMYFIPGGVMIYCYYNIFATVKSGDKQFGKAVKEMAHEDVKNK 0
0 AQQERQRKNEIKTAKIAFIVISLFMSAWTPYAVVSALGTLGYQDLVTPYLQSIPAMFAKSSAVYSPI 1
2 VYAITYPKFREAVKKHIPCLSGCLPASEEETKTKTRGQSSASASMSMTQTTAPV 0
0 HDPQASVDSGSSVSVDDSSGVSRQDTMMVK 0
0 VEVDKRMEKAGGGAADAAPQEGASVSTVSAQIEVRPSGKVTTKADVISTPQTAHGLSASPVPK 0
0 VAELGSSATLESAAIPGKIPTPLPSQPIAAPIERHMAAMADEPPPKPRGVATTVNVRRTESGYDRSQDSQRKK 0
0 VVGDTHRSRSFNTTKDHFASEQPAALIQPKELYSDDTTKKMARQSSEKHEYDNPAFDEGITEVDTDSENETEGSYDMLSVRFQAMAEEPPVETYRKASDLAINLGKASLMLSEAHDETVL* 0

>MEL1b_braBel Branchiostoma floridae Amphiop6 melanopsin approx Gq
0 MSPNLTNTSLLPNRTDRPELSPADVTMQLVFGSMMLVFGLIGVVGNAVALYAFCR 2
1 SRSLRRPKNYLIANLCLTDMVVCLVYSPIIVTRSLSHG 2
1 LPSKESCIVEGFVVGLGSIVSICSLAGIAVERYVTITQPIKSLSILTHRALLGAVSAVWVYAFLLAFPPLVGWGRYVSEESKISCTFDYLSTDDATRAHVIVLVIGAFGLPFS
VITYCYVRSFATVRKCTKERKQMSPLAKSDSRSEVKAAVNSFVITTSFCLCWCPYAVVATMGVSGFTVHSHAVFIAALLAKLSVLFNPVAYVLSIP 1
2 NSNVNIESTELTVPYSASRESCLLSRAATERLAGRSPSLTDIVREFGLQQTASHRE

>MEL1b_braBel Branchiostoma belcheri Amphiop6 melanopsin AB050611  Gq
0 MSSNLTNVSLVANRTDQTELSPTDVTMQLIFGSMMLVFGLIGVVGNVVALYAFCR 2
1 TRSLRRPKNYVVANLCLTDMFVCLVYCPIVVSRSFSHG 2
1 FPSKESCIVEGFMVGVGSIASICSLAAIAVERYLSVTQPLKSLTILTQRKLLVAVLTVWVYSLLLAFPPLVGWGRYVREETYISCTFDYLSTDDATRAYVITLVMGAFGFPLL
TIAYCYIRVFTTARKHAEERKFMSPLKRPESRTEIKTAVTACVITTSFCLCWCPYAVVATLGISGVSVQQQTVFSAALLAKLTVIINPIVYVLSIPNFRKALFAQEREKYASED
VVLTSLPGKTRRMKKVERSQSSNSNVVIEVKESSMAYSTSRESCLLSRAATKRLAGKTKSIVDLVDEFGLQETAPHKESLV*

>MEL2_galGal melanopsin2 GRID2 SMARCAD1 PGDS MEL2 SEC24B COL25A1
0 MGTQPHSVTKSEIPDHVLYTVGTCVLVIGSIGIIGNLLVLYAFYS 2
1 NKKLRTPQNFFIMNLAVSDFLMSASQAPICFVNSLHREWILGDI 1
2 GCDLYAFCGALFGITSMMTLLAISVDRYLVITKPLRSIQWTSKKRTIQIIAAVWLYSLGW 1
2 SVAPLLGWSSYVPEGLMISCTWDYVTYSPANRSYTMILCCCVFFIPLIIILHCYLFMFLAIRSTGR 2
1 DVQKLGSCSRKSFLSQSMKNEWKLAKIAFVVIIVYVLSWSPYACVTLIAWAG 2
1 RGNTLTPYSKSVPAVIAKASAIYNPIIYAIIHPRYRK 2
1 TIHNAVPCLRFLIRISKNDLLRGSINESSFRTSLSSHQSLAGRTKNTCVSSVSTGEA 0
0 NWSDVELDTVEPAHEKLQPRRSHSFSSSLRQKRDLLPDSYSCSEETEEK 0
0 VSLSSSYLEKVLGRSAFPSSPVALVTSSLRAASLPVGLNSSSASRGAGSDISQMKTEESHNNGGLDSIVSNTVPQIIIIPTSETNLFQEEPEEEETELFHFHDKKNNLLDLEGLSSSTEFLEAVEKFLS* 0

>MEL2_anoCar melanopsin2 frag GRID2 SMARCAD1 MEL2 PDILM5 BMPR1B UNC5B
0 MGPHHRTKVDVPDHVLYTVGSCVLVIGCIGITGNLLVLYAFYS 2
1 NKRLRTPPNYFIMNLAVSDFLMSATQAPICFLNSMHKEWVLGDI 1
2 GCNLYAFCGALFGITSMITLLAISVDRYCVITKPLQSIKRTSKKRTCIIIVFVWLYSLGWSVCPLFGW 1
2 SSYIPEGLMISCTWDYVTYSPANRSYTMMLCCCVFFIPLVIIFHCYIFMFLAIRSTGR 2
1 RKSSISHSIKSEWKLAKIAFVAIVVFVLSWSPYACVTLISWAG 2
1 TLTPYSKSVPAVIAKASAIYNPIIYAIIHPRYRK 2
1 TIRSAVPCLRFLIPISKSDLSTSSMSESSFRASVSSRHSFSYRNKSTYISSISAKET 0
0 TWCDVELDPVESGHKKLQAYRSNSFSAKGVAEEESGLLLRTNNCNVPARKK 0

>MEL2_xenLae Xenopus laevis melanopsin (Xmop) SMARCAD1 
0 MDLGKTVEYGTHRQDAIAQIDVPDQVLYTIGSFILIIGSVGIIGNMLVLYAFYR 2
1 NKKLRTAPNYFIINLAISDFLMSATQAPVCFLSSLHREWILGDI 1
2 GCNVYAFCGALFGITSMMTLLAISINRYIVITKPLQSIQWSSKKRTSQIIVLVWMYSLMWSLAPLLGW 1
2 SSYVPEGLRISCTWDYVTSTMSNRSYTMMLCCCVFFIPLIVISHCYLFMFLAIRSTGR 2
1 NVQKLGSYGRQSFLSQSMKNEWKMAKIAFVIIIVFVLSWSPYACVTLIAWAG 2
1 HGKSLTPYSKTVPAVIAKASAIYNPIIYGIIHPKYRE 2
1 TIHKTVPCLRFLIREPKKDIFESSVRGSIYGRQSASRKKNSFISTVSTAET 0
0 VSSHIWDNTPNGHWDRKSLSQTMSNLCSPLLQDPNSSHTLEQTLTWPDDPSPKEILLPSSLKSVTYPIGLESIVKDEHTNNSCVR
NHRVDKSGGLDWIINATLPRIVIIPTSESNISETKEEHDNNSEEKSKRTEEEEDFFNFHVDTSLLNLEGLNSSTDLYEVVERFLS* 0

>MEL2_danRer Danio rerio (zebrafish) FLJ39155 PDILM5
0 MEPQRQIYKRLDVPDHVHYIIAFLILIIGTLGVSGNALVMFAFYR 2
1 NKKLRSLPNYFIMNLAVSDFLMAITQSPIFFINCLYKEWMFGEL 1
2 GCKIYAFCGALFGITSMINLLAISIDRYLVITKPLQTIQWNSKRRTGLAILCIWLYSLAWSLAPLIGW 1
2 GSYIPEGLMTSCTWDYVSPSPANKSYTMMLCCFVFFIPLSIILYCYLFMFLSVRQASR 2
1 QKSSFVKQQSMRSEWKLAKIAAVVIVVYVLSWAPYACVTLVAWAG 2
1 LTPYSKTLPAVLAKSSAIYNPFIYAIIHNKYRA 2
1 TLAEKVPGLSCLSRSQKDGLSSSTNSDASAQDSSVSRQSSVSKNRLHSTMVQ* 0

>MEL2_tetNig frag +BMPR1B
0 MEPKDTHITSSFFSKVDVPDHVHYIIAFFVFVIGILGITGNVLVIFAFYS 2
1 NKKLRSLPNYFIVNLAVSDLLMASTQSPIFFINLYKEWMFGET 1
2 ACKMYAFCGALFGITSMINLLAISVDRYVVITKPLQTIRRSSKRRTALAILMVWLYSLAWSLAPLVGW 1
2 GSYIPEGLMTSCTWDYVTYTLANRSYTMMLCCFVFFIPLAIILCCYLLMFLAIRKTSR 2
1 RKSTLIQQKSIRSEWKLAKIAFVVIVVYVLSWSPYACVTLISWAG 2
1 TLTPYSKSVPAVIAKASAIYNPIIYAIIHPRYRK 2
1 TIRSAVPCLRFLIPISKSDLSTSSMSDSSFRSALSCRHSYRSRSTYISSISAKET 0
0 TWCDVELDPVESGHKKLQAYRSNSFSAKGVAEEESGLLLRTNNCNVPARKK 0

>MEL2_gasAcu Gasterosteus aculeatus KNTC2 FLJ39155  PDLIM5 BMPR1B
0 MEPDNAHTQRSFINKVDVPDHAHYIVAVFVVVIGTLGITGNALVMLAVYS 2
1 NKKLRNLPNYFIMNLAVSDFLMAFTQSPIFFINCLYKEWAFGET 1
2 GCKIYAFCGALFGIASMINLLAISIDRYLVITKPLQAIHWGSKRRTTLAILLVWLYSLAWSLAPLVGW 1
2 GSYIPEGLMTSCTWDYVTYTLANRSYTMMLCCFVFFIPLGIILYCYLFMFLAIRKTSR 2
1 RKSTLIKQKSMKSEWKLAKIAFVVIVVYVLSWSPYACVTLISWAG 2
1 ILSPYSKAVPAIIAKASAIYNPFIYAIIHNKYRM 2
1 TLAAKFPCLRFLSPTPRKDTSSSISESSYRDSVISRQSTASRTHFITACPDTVN 0

>RHAB_plaDum Platynereis dumerilii (clam worm) rhabdomeric opsin Gq AJ316544 runs as melanopsin unavailable genomically
MSRSEVLVPGSMSLDGLLTTAHPIGNDSIETILHPYWQQFDIENTIPDSWHYAVAAWMTFFGILGVSGNLLVVWTFLKTKSLRTAPNMLLVNLAIGDMAF
SAINGFPLLTISSINKRWVWGKLWRELYAFVGGIFGLMSINTLAWIAIDRFYVITNPLGAAQTMTKKRAFIILTIIWANASLWALAPFFGWGAYIPEGFQ
TSCTYDYLTQDMNNYTYVLGMYLFGFIFPVAIIFFCYLGIVRAIFAHHAEMMATAKRMGANTGKADADKKSEIQIAKVAAMTIGTFMLSWTPYAVVGVFG
MIKPHSEMFIHPLLAEIPVMMAKASARYNPIIYALSHPKFRAEIDKHFPWLLCCCKPKPKAQLPSSTTKGSIASKTEADTSV*

>RHAB1_apiMel Apis mellifera long wavelength sensitive opsin 1 (Lop1) NM_001077825 compound eyes
MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQY
PPLNPMWHGILGFVIGMLGFVSVMGNGMVVYIFLSTKSLRTPSNLFVINLAISDFLMM
FCMSPPMVINCYYETWVLGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG
KPLSINGALIRIIAIWLFSLGWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLV
CYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKL
AKVALMTISLWFMAWTPYLVINFSGIFNLVKISPLFTIWGSLFAKANAVYNPIVYGIS
HPKYRAALFAKFPSLACAAEPSSDAVSTTSGTTTVTDNEKSNA*

>RHAB2_apiMel Apis mellifera long wavelength sensitive opsin 2 (Lop2) NM_001077825 ocelli
MDTLNITTSFFIEVMPSNISTLTTTGPQFARQLMRFNNQTVVSK
VPEEMLHLIDLYWYQFPPLDPLWHKILGLVMIILGIMGWCGNGVVVYVFIMTPSLRTP
SNLLVVNLAFSDFIMMGFMCPPMVICCFYETWVLGSLMCDIYAMVGSLCGCASIWTMT
AIALDRYNVIVKGMSGTPLTIKRAMLQILGIWLFGLIWTILPLVGWNRYVPEGNMTAC
GTDYLSQDWTFKSYILVYSFFVYYTPLFTIIYSYYFIVSAVAAHEKAMKEQAKKMNVT
SLRSGDNQNTSAEAKLAKVALTTISLWFMAWTPYLVINYIGIFNRSLITPLFTIWGSL
FAKANAIYNPIVYGISHPKYRAALKEKLPFLVCGSTEDQTAATAGDKASEN*

>RHAB3_apiMel Apis mellifera UV-sensitive opsin BK005513
MSNDSIHWEARYLPAGPPRLLGWNVPAEELIHIPEHWLVYPEPN
PSLHYLLALLYILFTFLALLGNGLVIWIFCAAKSLRTPSNMFVVNLAICDFFMMIKTP
IFIYNSFNTGFALGNLGCQIFAVIGSLTGIGAAITNAAIAYDRYSTIARPLDGKLSRG
QVILFIVLIWTYTIPWALMPVMGVWGRFVPEGFLTSCSFDYLTDTNEIRIFVATIFTF
SYCIPMILIIYYYSQIVSHVVNHEKALREQAKKMNVDSLRSNANTSSQSAEIRIAKAA
ITICFLYVLSWTPYGVMSMIGAFGNKALLTPGVTMIPACTCKAVACLDPYVYAISHPK
YRLELQKRLPWLELQEKPISDSTSTTTETVNTPPASS*

>RHAB4_apiMel Apis mellifera blue-sensitive opsin (Blop)
MLLHNKTLAGKALAFIAEEGYVPSMREKFLGWNVPPEYSDLVHP
HWRAFPAPGKHFHIGLAIIYSMLLIMSLVGNCCVIWIFSTSKSLRTPSNMFIVSLAIF
DIIMAFEMPMLVISSFMERMIGWEIGCDVYSVFGSISGMGQAMTNAAIAFDRYRTISC
PIDGRLNSKQAAVIIAFTWFWVTPFTVLPLLKVWGRYTTEGFLTTCSFDFLTDDEDTK
VFVTCIFIWAYVIPLIFIILFYSRLLSSIRNHEKMLREQAKKMNVKSLVSNQDKERSA
EVRIAKVAFTIFFLFLLAWTPYATVALIGVYGNRELLTPVSTMLPAVFAKTVSCIDPW
IYAINHPRYRQELQKRCKWMGIHEPETTSDATSAQTEKIKTDE*



Here are those sequences aligned to show rare genomic events such as indels and intron gains and losses:

>RHO1_homSap LAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWS
>RHO1_monDom LAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTMTLYTSLHGYFVFGPTGCNLEGFFATLG GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIIGVAFTWVMALACAFPPLIGWS
>RHO1_ornAna LAAYMFMLIMLGFPINFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVLGGFTTTLYTSLHGYFVFGPTGCNIEGFFATLG GEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACALPPLVGWS
>RHO1_galGal LAAYMFMLILLGFPVNFLTLYVTIQHKKLRTPLNYILLNLVVADLFMVFGGFTTTMYTSMNGYFVFGVTGCYIEGFFATLG GEIALWSLVVLAVERYVVVCKPMSNFRFGENHAIMGVAFSWIMAMACAAPPLFGWS
>RHO1_anoCar LAAYMFLLILLGFPINFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVLMGFTTTMYTSMNGYFIFGTVGCNIEGFFATLG GEMGLWSLVVLAVERYVVICKPMSNFRFGETHALIGVSCTWIMALACAGPPLLGWS
>RHO1_xenTro LAAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMHGYFIFGQTGCYIEGFFATLG GEMALWSLVVLAIERYVVVCKPMANFRFGENHAIMGVVFTWIMALSCAAPPLFGWS
>RHO1_danRer VAAYMFFLIITGFPVNFLTLYVTIEHKKLRTPLNYILLNLAIADLFMVFGGFTTTMYTSLHGYFVFGRLGCNLEGFFATLG GEMGLKSLVVLAIERWMVVCKPVSNFRFGENHAIMGVAFTWVMACSCAVPPLVGWS
>RHO1_Raja   LAAYMFFLILTGLPVNFLTLFVTIQHKKLRQPLNYILLNLAVSDLFMVFGGFTTTIITSMNGYFIFGPAGCNFEGFFATLG GEVGLWCLVVLAIERYMVVCKPMANFRFGSQHAIIGVVFTWIMALSCAGPPLVGWS
>RHO1_lamp1  LAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAVANLFMVLFGFTLTMYSSMNGYFVFGPTMCNFEGFFATLG GEMSLWSLVVLAIERYIVICKPMGNFRFGSTHAYMGVAFTWFMALSCAAPPLVGWS
>RHO1_lamp2  LAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAVSNLFMILFGFTTTMYTSMNGYFVFGPTMCSIEGFFATLG GEVSLWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVALTWVMALSCAAPPLLGWS
>RHO1_lamp3  LAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWS
>RHO2_galGal VCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWS
>RHO2_anoCar VCCYIFFLIFTGLPINILTLLVTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFIFGPIGCAIEGFFATLG GQVALWSLVVLAIERYIVVCKPMGNFRFSATHALMGISFTWFMSFSCAAPPLLGWS
>RHO2_Gekko  LSFYMFFLIAAGMPLNGLTLFVTFQHKKLRQPLNYILVNLAAANLVTVCCGFTVTFYASWYAYFVFGPIGCAIEGFFATIG GQVALWSLVVLAIERYIVICKPMGNFRFSATHAIMGIAFTWFMALACAGPPLFGWS
>RHO2_Lat    LCAYMFLLIILGFPINFLTLLVTFKHKKLRQPLNYILVNLAVASLFMVVFGFTVTFYSSLNGYFVLGPMGCAMEGFFATLG GQVALWSLVVLAIERYIVVCKPMGNFRFASSHAIMGIAFTWIMALACAAPPLVGWS
>RHO2_Geo    ISAYVFTLILIGFPVNFMTLFVTFKLKKLRQPLNFILVNLCVADLLMIMFGFTTTFYTAMNGYFVFGPTGCNIEGFFATLG GEVSLWSLVMLAIERYIVVCKPMGNFRFATTHAALGVVFTWVMASACAVPPLVGWS
>SWS1_homSap QAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVA GLVTGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWS
>SWS1_macDom QTVFMGFVFCAGTPLNAVVLVATLRYKKLRQPLNYILVNVSLCGFIFCIFAVFTVFISSSQGYFIFGRHVCAMEAFLGSVA GLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWVIGIGVSIPPFFGWS
>SWS1_galGal QTAFMGIVFAVGTPLNAVVLWVTVRYKRLRQPLNYILVNISASGFVSCVLSVFVVFVASARGYFVFGKRVCELEAFVGTHG GLVTGWSLAFLAFERYIVICKPFGNFRFSSRHALLVVVATWLIGVGVGLPPFFGWS
>SWS1_Taenio QTIFMGLVFVAGTPLNAIVLIVTIKYKKLRQPLNYILVNISVSGLMCCVFCIFTVFIASSQGYFVFGKHMCAFEGFAGATG GLVTGWSLAFLAFERYIVICKPFGNFRFNSRHALLVVAATWIIGVGVAIPPFFGWS
>SWS1_Gekko  QTAFMGFVFFVGTPLNAIILFAIVKYKKLRQPLNYILVNISAAGFLFCVVAVFTVFISSSQGYFIFGKHICALEAFLGSLA GLVTGWSLAFLALERYIVICKPFGNFRFSAKHASLVVAATWFIGIGVSIPPYFGWS
>SWS1_Utasta QTAFMGFVFFAGTPLNAIILIVTVKYKKLRQPLNYILVNISFAGFLFCVFSVFTVFLASSQGYFFFGRHICALEAFLGSVA GLVTGWSLAFLAFERYIVICKPFGNFRFNSKHALLVVAATWFIGIGVSIPPFFGWS
>SWS1_Xenlae QAIFMGMVFLIGTPLNFIVLLVTIKYKKLRQPLNYILVNITVGGFLMCIFSIFPVFVSSSQGYFFFGRIACSIDAFVGTLT GLVTGWSLAFLAFERYIVICKPMGNFNFSSSHALAVVICTWIIGIVVSVPPFLGWS
>SWS1_Danio  QAAFMGFVFIVGTPMNGIVLFVTMKYKKLRQPLNYILVNISLAGFIFDTFSVSQVSVCAARGYYSLGYTLCSMEAAMGSIA GLVTGWSLAVLAFERYVVICKPFGSFKFGQGQAVGAVVFTWIIGTACATPPFFGWS
>SWS1_Oryzia QAAFMGFVFFVGTPLNFVVLLATAKYKKLRVPLNYILVNITFAGFIFVTFSVSQVFLASVRGYYFFGQTLCALEAAVGAVA GLVTSWSLAVLSFERYLVICKPFGAFKFGSNHALAAVIFTWFMGVGCACPPFFGWS
>SWS1_Geotri QAAFMGFVFICGTPLNAIVLVVTIKYKKLRQPLNYILVNISAAGLVFCLFSISTVFVASMQGYFFLGPTICALEAFFGSLA GLVTGWSLAFLAAERYIVICKPFGNFRFGSKHALVAVGLTWMLGLSVALPPFFGWS
>SWS2_ornAna LAAFMFLLITLGFPINLLTVICTIKYKKLRSHLNYILVNLAVSNMLVVCVGSATAFYSFAHMYFVLGPTACKIEGFAATLG GMVSLWSLAVIAFERFLVICKPLGNLSFRGTHAIFGCAATWVFGLAASLPPLFGWS
>SWS2_galGal MAAFMFLLIALGVPINTLTIFCTARFRKLRSHLNYILVNLALANLLVILVGSTTACYSFSQMYFALGPTACKIEGFAATLG GMVSLWSLAVVAFERFLVICKPLGNFTFRGSHAVLGCVATWVLGFVASAPPLFGWS
>SWS2_Taenio MAAFMFLLVLLGVPINALTVLCTAKYKKLRSHLNYILVNLAVANLLVVCVGSTTAFYSFSQMYFALGPLACKIEGFTATLG GMVSLWSLAVVAFERFLVICKPLGNFTFRGSHAVLGCAITWIFGLIASLPPLFGWS
>SWS2_Utasta MAAFMFLLIILGVPINVLTIFCTFKYKKLRSHLNYILVNLAVSNLLVVCIGSTTAFYSFAQMYFSLGPTACKIEGFAATLG GMVSLWSLAVVAFERFLVICKPLGNFSFRGTHAIIGCIITWVFGLVASLPPLFGWS
>SWS2_Xenopu ISAFMLFTIIFGFPLNLLTIICTVKYKKLRSHLNYILVNLAVANLIVICFGSTTAFYSFSQMYFSLGTLACKIEGFTATLG GIIGLWSLAVVAFERFLVICKPMGNFTFRESHAVLGCILTWVIGLVAAIPPLLGWS
>SWS2_Danio  MSAFMLFLFIAGTAINVLTIVCTIQYKKLRSHLNYILVNLAISNLWVSVFGSSVAFYAFYKKYFVFGPIGCKIEGFTSTIG GMVSLWSLAVVALERWLVICKPLGNFTFKTPHAIAGCILPWCMALAAGLPPLLGWS
>SWS2_Takifu MSAFMFFLFVAGTGINVLTIACTIQYKKLRSHLNYILVNLAFSNLLVTTVGSFTCFCCFFVRYMIVGPLGCKIEGFAATLG GMVSLWSLAVVAFERWLVVCKPLGNFIFKPDHAIVCCIFTWFFALIISAPPLFGWS
>SWS2_Geotri MSAFMLFLVLAGFPLNFLTVFVTIKYKKLRSHLNYILVNLAIANLIVVCCGSTLAFYSFMHKYFILGPLFCKMEGFTATLG GMLSLWSLAVLAFERCLVICKPFGNIAFRGTHALIRCGFAWAAAIAASTPPLFGWS
>LWS_ornAna  TSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFILGHPMCVLEGYTVSLC GITGLWSLSIISWERWIVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWS
>LWS_galGal  TSLWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGHPMCVVEGYTVSAC GITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAWTAPPIFGWS
>LWS_anoCar  TSVWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISGYFILGHPMCVLEGYTVSTC GISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSWVWSAVWTAPPVFGWS
>LWS_Lithoch ATLWMFVVVVLSVFTNGLVLVATMKFKKLRHPLNWILVNLAIADLGETVFASTISVCNQFFGYFILGHPMCIFEGYVVSVC GIAALWSLTIISWERWIVVCKPFGNVKFDAKWATAGIVFSWVWAAVWCAPPIFGWS
>LWS_Gastero STLWMFIVVALSVFTNGLVLVATAKFKKLQHPLNWILVNLAIADLGETVFASTISVCNQFFGYFILGHPMCVFEGYVVSVC GITALWSLTIISWERWIVVCKPFGNVKFDAKWATAGIVFSWIWSAVWCAPPIFGWS
>LWS_Petrom  TSVWMIIVVVLSLFSNGLVLVATVKFKKLRHPLNWIIVNLAIADILETIFASTISVCNQVYGYFILGHPMCVFEGYVVSTC GIAGLWSLAIISWERWMVVCKPFGNIKFDGKIATILIVFSWVWPASWCSLPIFGWS
>LWS_lamprey TSVWMIIVVVLSLFTNGLVLVATMKFKKLRHPLNWILVNLAIADILETIFASTISVCNQVFGYFILGHPMCVFEGYVVSTC GIAGLWSLAIISWERWMVVCKPFGNIKFDGKIAIILIVFSWVWPACWCSLPIFGWS
>LWS_Geotria TSFWMIIVVILSLFTNGLVLVATLKFKKLRHPLNWILVNLAIADIGETIFASTVSVVNQIFGYFILGHPLCVFEGFTVSVC GITALWSLAIISFERWMVVCKPFGNLKFDGKVAIVLIIFSWAWSAGWCAPPIFGWS
>PIN_galGal  VAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLT GIVGLWSLAILALERYVVVCRPLGDFQFQRRHAVSGCAFTWGWALLWSTPPLLGWS
>PIN_UtaSta  VAVLMGLVVVSAAFVNGLVIVVSIQYKKLRSPLNYILVNLAIADLLVTSFGSTLSFANNIYGFFVLGQTACEFEGFMVSLT GIVGLWSLAILAFERYLVICKPVGDFRFQQRHAVFGCVFTWMWSLVWTLPPLFGWS
>PIN_pheMad  LAALMGVVVLSASLANGLVIAVSVRFKRLRSPLNYILVNLATADLLVTFFGSIISFVNNAVGFFVFGKTACRFEGFMVSLT GIVGLWSLAILAFERYLVICKPVGDFQFQRRHAVIGCLYTWGWSLIWTVPPLFGWS
>PIN_podSic  VAVLMGLVVISATLVNGLVIVVSVQFKKLRSPLNYVLVNLAVADLLVTFFGSTISFVNNAQGFFIFGQATCEFEGFMVSLT GIVGLWSLAILAFERYLVICKPVGDFRFPARHAVLGCAFTWGWSFVWTVPPLLGWS
>PIN_xenTro  VAAVMCMVVILAFFVNGLVIVVTLKYKKLRSPLNYILVNLAIANLLVTIFGSSVSFSNNVVGYFFMGKTMCEFEGFMVSLT GIVGLWSLAILAFERYLVICKPMGDFRFQQKHAILGCSFTWVWSFIWTSPPLFGWC 
>PIN_bufJap  VAVLMGMVVFLAFFVNGMVIVVSLKYKKLRSPLNYILVNLAVADILVTMFGSTVSFHNNIFGFFTLGKLVCELEGFVVSLT GIVGLWSLAILAFERYIVICKPMGDFRFQQRHAVMGCAFTWIWAFLWTSPPLIGWC
>VAOP_galGal VAAVMFVVTSLSLAENLAVILVTFKFKQLRQPVNYVIVNLSVADFLVSLTGGTISFLANLKGYFYMGHWACVLEGFAVTFF GIVALWSLALLAFERYIVICRPVGNMRLRGKHAAQGIAFVWTFSFIWTIPPTMGWS
>VAOP_anoCar ISALMFVVTLFSLSENFTVILVTIKFKQLRQPLNYVIVNLSVADFLVSLIGGTISFSTNLKGYFYMGHWACVLEGFAVTFF GIVALWSLALLAFERYVVICRPLGNMRLNGKHAALGVAFVWIFSFIWTVPPTMGWS
>VAOP_xenTro LAALMFVVTSLSIAENFIVILVTAKFKQLRQPLNYIIVNLSVADFLVSVIGGTISIATNSRGYFYLGSWACVLEGFAVTFF GIVALWSLSVLAFERYIVICRPLGNLRLQGKHSALAIIFVWVFSFVWTIPPTMGWS
>VAOP_danRer LAALMFVVTALSLSENFTVMLVTFRFQQLRQPLNYIIVNLSLADFLVSLTGGSISFLTNYHGYFFLGKWACVLEGFAVTFF GIVALWSLAVLAFERFFVICRPLGNIRLRGKHAALGLVFVWSFSFIWTVPPVLGWS
>VAOP_rutRut LATLMFVVTAASLSENFAVMLVTFRFTQLRKPLNYIIVNLSLADFLVSLTGGTISFLTNYHGYFFLGKWACVLEGFAVTYF GIVALWSLAVLAFERFFVICRPLGNIRLRGKHAALGLLFVWTFSFIWTIPPVLGWS
>VAOP_Petro  LAALMGTITALSLGENFAVIVVTARFRQLRQPLNYVLVNLAAADLLVSAIGGSVSFFTNIKGYFFLGVHACVLEGFAVTYF GVVALWSLALLAFERYFVICRPLGNFRLQSKHAVLGLAVVWVFSLACTLPPVLGWS
>PPIN_anaCar IAIIMATSCTLSVILNTAVIAITIKYRQLRQPINYSLVNLAIADLGAALLGGSLNVETNAVGYYNLGRVGCVTEGFAMAFF GIVALCTIAVIAVDRAIVIAKPMGTITFTTRKAMIGVAVSWIWSLVWNTPPLFGWG
>PPIN_Xenop  LALIMAVFCAAALFLNVTVIVVTFKYRQLRHPINYSLVNLAIADLGVTVLGGALTVETNAVGYFNLGRVGCVIEGFAVAFF GIAALCTIAVIALDRVFVVCKPMGTLTFTPKQALAGIAASWIWSLIWNTPPLFGWG
>PPIN_Ictal  LSIIMALSSTFGIILNMVVIIVTVRYKQLRQPLNYALVNLAVADLGCPVFGGLLTAVTNAMGYFSLGRVGCVLEGFAVAFF GIAGLCSVAVIAVDRYMVVCRPLGAVMFQTKHALAGVVFSWVWSFIWNTPPLFGWG
>PPIN_Danio  LAVIIGVFSVCGVILNVTVITVTLKYKQLRQPLNFALVNLAVADLGCAVFGGLPTVVTNAMGYFSLGRVGCVLEGFAVAFF GIAALCSVAVIALERCMVVCRPVGSISFQTRHAVFGVAVSWLWSFIWNTPPLFGWG
>PPIN_Oncor  LAVIIGVFSVSGVCMNVLVIMVTMRHRKLRQPLNYALVNLAVADLGCALFGGLPTMVTNAMGYFSMGRLGCVLEGFAVAFF GIAGLCSVAVIAVDRYVVVCRPMGAVMFQTRHAVGGVVLSWVWSFLWNTPPLFGWG
>PPINa_Ciona LCVYMTFVFLLSCSLNILVIVATLKNKVLRQPLNYIIVNLAVVDLLSGFVGGFISIAANGAGYFFWGKTMCQIEGYFVSNF GVTGLLSIAVMAFERYFVICKPFGPVRFEEKHSIFGIVITWVWSMFWNTPPLIFWD
>PPINb_Ciona LAVYMTFIFLLAVSLNGFVIIATMKNKKLRQPLNYIIINLSIADFLSGLVGGFIGMISNSAGYFYFGKTVCILEGYIVSVA GVCGLMSISVMAFERYFVVCKPYGPFTLTNTHAALGIGFTWTWSVLWSTPGLIWLD
>PPIN_lamp   LAVIMAVFTIASLVLNSTVVIVTLRHRQLRHPLNFSLVNLAVADLGVTVFGASLVVETNAVGYFNLGRVGCVIEGFAVAFF GIAALCTIAVIAVDRFVVVCKPLGTLMFTRRHALLGIAWAWLWSFVWNTPPLFGWG
>PARIE_Utast LAFLMFLNALFSIFNNSLVIAVTLKNPQLRNPINIFILNLSFSDLMMSLCGTTIVIATNYYGYFYLGRKFCIFQGFAVNYF GIVSLWSLTILA YERYNVV--CQPLGTLQMSTKR GYQLLGFIWVFCLFWAVVPLFGWS
>PARIE_Anole LAFLMFINALFSLFNNFLVIAVTLKNPQLRNPINIFILNLSFSDLMMSICGTTIVIATNYHGYFYLGRRFCIFQGFAVNYF GIVSLWSLTILA YERYNVV--CQPLGTLQMSTQR AYQLLGFIWVFCLFWAVVPLFGWS
>PARIE_Xenop LSFLMFLNAVFSICNNAIVILVTLKHPQLRNPINIFILNLSFSDLMMALCGTTIVVSTNYHGYFYLGKQFCIFQGFAVNYF GIVSLWSLTLLA YERYNVV--CEPIGALKLSTKR GYQGLVFIWLFCLFWAIAPLFGWS
>ENCEPH_braB VAGVIAIIGVVGFVSNGAVVVLFLKFPQLRTPFNLLLLNMAVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF GLVSLISLAVIS FLRYRMVVKPKGPGSSYLTYTK VGLAILFIYLYCLLWTTLPIAGWS
>ENCEPH_homS LALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF GIVSIATLTVLA YERYIRVV-----HARVINFSW AWRAITYIWLYSLAWAGAPLLGWN
>ENCEPH_monD LALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF GIVSIMTLTVLA YERYNRIV-----HAKVINFSW AWRAITYIWLYSLVWTGAPLLGWN
>ENCEPH_galG LALLIATIGTLGVCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVCGVSLTFMSCLRSRWVWDAAGCVWDGFSNSLF GIVSIMTLTVLA YERYIRVV-----HAKVIDFSW SWRAITYIWLYSLAWTGAPLLGWN
>ENCEPH_anoC LALLVAAIGLLGLCNNLLVLVLYAKFKRLRTPTHLFLVNISLSDLLVSLFGVSFTFGSCLRHRWVWDAAGCVWDGFSNSLF GIVSIMTLTVLA YERYIRVV-----HARVIDFSW SWRAITYIWLYSLAWTGAPLLGWN
>ENCEPH_xenT LALIVATVGFLGLVNNLLVLILYCKFKRLQTPTNLLFFNTSLCHFVFSLLAITFTFMSCVRGSWAFSVEMCVFHGFSKNLL GIVSFGTLTVVA YERYARVV-----YGKYVNSSW SKRSITFVWVYSLAWTGFPLIGWN
>ENCEPH_braB IATGLALIGLVGSMNNFVVILLIGCHRQLRTPFNLLLLNVSVADLLVSVCGNTLSFASAVQHRWLWGRPGCVWYGFANSLF GIVSLVTLSALA FERYCVVV----RSSEMLTYKS SLGMIAFIWMYSLLWTSLPLLGWS
>ENCEPH_braF IATCLALIGFVGFTNNFVVILLIGCHRQLRTPFNLLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANSLF GIVSLVTLSALA FERYCVVV----RSSDMLTYKS SLVVITFIWLYSLLWTSLPLLGWS
>ENCEPH2_Api AIALGFIGFFGFTANLLVAIVIVKDAQILWTPVNVILFNLVFGDFLVSIFGNPVAMVSAATGGWYWGYKMCLWYAWFMSTL GFASIGNLTVMA VERWLLVA----RPMQALSIRH AVILASFVWIYALSLSLPPLFGWG
>ENCEPH1_Ano AAVTLFFIGFFGFFLNIFVIALMYKDVQLWTPMNIILFNLVCSDFSVSIIGNPLTLTSAISHRWLYGKSICVAYGFFMSLL GIASITTLTVLS YERFCLIS--RPFAAQNRSKQG ACLAVLFIWSYSFALTSPPLFGWG
>ENCEPH2_Ano SAVTLFFIGFFGFFLNLFVIALMCKDMQLWTPMNIILFNLVCSDFSVSIIGNPLTLTSAISHRWIFGRTLCVAYGFFMSLL GITSITTLTVLS YERYCLIS--RPFSSRNLTRRG AFLAIFFIWGYSFALTSPPLFGWG
>CILL2_Platy AIYLCIVGVIGTLSNGVIMYLYFKDKSLRSPMNLLFVNLAMSDFTVAFFGAMFQFGLTCTRKYMSPGMALCDFYGFITFLG GLASEMNLFIIS VERYLAVV--RPFDVGNLTNRR VIAGGVFVWLYSLVFAGGPLVGWS
>CILL1_Platy AAYLFFIACLGVSLNVLVLVLFIKDRKLRSPNNFLYVSLALGDLLVAVFGTAFKFIITARKTLLREEDGFCKWYGFITYLG GLAALMTLSVIA FVR CLAV-LRLGSFTGLTTRM GVAAMAFIWIYSLAFTLAPLLGWN
>MEL1_homSap LGTVILLVGLTGMLGNLTVIYTFCRSRSLRTPANMFIINLAVSDFLMSFTQAPVFFTSSLYKQWLFGETGCEFYAFCGALF GISSMITLTAIA LDRYLVIT-RPLATFGVASKRR AAFVLLGVWLYALAWSLPPFFGWS
>MEL1_smiCra IGATILVVGFTGVLGNLLVIYTFCRSRSLRTPANMFIINLAISDFFMSFTQAPVFFASSLYERWIFGEKGCEFYAFCGALF GITSMITLMVIA LDRYFVIT-RPLASIGMISKKK TGLILLGVWLYSLAWSLPPFFGWS
>MEL1_galGal IGTVILIVGITGTLGNFLVIYAFCRSRTLQKPANIFIINLAVSDFLMSITQSPVFFTNSLHKRWIFGEKGCELYAFCGALF GITSMITLMVIA LDRYFVIT-KPLASVRVMSKKK ALIILVGVWLYSLAWSLPPFFGWS
>MEL1_xenTro VGAVILAVGITGMLGNFLVIYAFCRSRSLRSPANMFIINLAITDFLMSVTQAPVFFATSLHKRWIFGEKGCELYAFCGALF GITSMITLMVIA VDRYFVIT-RPLTSIGVMSKKR AVLILSGVWLYSLAWSLPPFFGWS
>MEL1a_Bran  VGTAVFCIGCCGMFGNAVVVYSFIKSKGLRTPANFFIINLALSDFLMNLTNMPIFAVNSAFQRWLLSDFACELYGFAGGLF GCLSINTLMAIS MDRYLVIT-KPFLVMRIVTKQR VMFAILLLWIWSLVWALPPLFGWS
>MEL2_anoCar VGSCVLVIGCIGITGNLLVLYAFYSNKRLRTPPNYFIMNLAVSDFLMSATQAPICFLNSMHKEWVLGDIGCNLYAFCGALF GITSMITLLAIS VDRYCVIT-KPLQSIKRTSKKR TCIIIVFVWLYSLGWSVCPLFGWS
>MEL2_xenLae IGSFILIIGSVGIIGNMLVLYAFYRNKKLRTAPNYFIINLAISDFLMSATQAPVCFLSSLHREWILGDIGCNVYAFCGALF GITSMMTLLAIS INRYIVIT-KPLQSIQWSSKKR TSQIIVLVWMYSLMWSLAPLLGWS
>NEUR_homSap AGFYLTIIGILSTFGNGYVLYMSSRRKKKLRPAEIMTINLAVCDLGISVVGKPFTIISCFCHRWVFGWIGCRWYGWAGFFF GCGSLITMTAVS LDRYLKIC--YLSYGVWLKRKH AYICLAAIWAYASFWTTMPLVGLG
>RGR_homSap  VLLVEALSGLSLNTLTIFSFCKTPELRTPCHLLVLSLALADSGISLNALVAATSSLLRVSHRRWPYGSDGCQAHGFQGFVT ALASICSSAAIA WGRYHHYC-----TRSQLAWNS AVSLVLFVWLSSAFWAALPLLGWG
>PER_homSap  VATYLIMAGMISIISNIIVLGIFIKYKELRTPTNAIIINLAVTDIGVSSIGYPMSAASDLYGSWKFGYAGCQVYAGLNIFF GMASIGLLTVVA VDRYLTIC--LPDVGRRMTTNT YIGLILGAWINGLFWALMPIIGWA
>PERa_Branc  VGLYLFVIGIIGTIENGITLATFSKFRSLRSPTTMLLVHLAIADLGICIFGYPFSGASSLRSHWLFGGVGCQWYGFNGMFF  

>PPIN2_cioSa LCVFMSFVFVLAVPLNLLVIVATYKNKVLRRPINYIIVNLAVADLTCSVVGGLLGVLNNGAGYYFLGKSVCIFEGYVMSVT  
>MEL_Platy                                                                                     GIFGLMSINTLA WIAIDRFYVITNPLGAAQTMTKKRAFIILTIIWANASLWALAPFFGWG
>MEL1b_Bran  IFGSMMLVFGLIGVVGNVVALYAFCRTRSLRRPKNYVVANLCLTDMFVCLVYCPIVVSRSFSHGFPSKESCIVEGFMVGVG - 
>MEL2_galGal CFVNSLHREWILGDIGCDLYAFCGALFGITSMMTLLAISVDRYLVITKPLRSIQWTSKKRTIQIIAAVWLYSLGWS

amino terminal alignment of imaging opsins:
((((RHO1,RHO2), SWS1),(LWS,SWS2),(PIN,VAOP)
                                     !!!    ***   !!!     **  ***   * *  *
>RHO1_homSap                        MNGTEGPNFYVPFSNATGVVRSPFEYPQY-YLAEPWQFSM LAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
>RHO1_monDom                        MNGTEGPNFYVPFSNKTGTVRSPFEEPQY-YLADPWQFSC LAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTMTLYTSLHGYFVFGPTGCNLEGFFATLG
>RHO1_ornAna                        MNGTEGQDFYIPMSNKTGVVRSPFEYPQY-YLAEPWQYSV LAAYMFMLIMLGFPINFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVLGGFTTTLYTSLHGYFVFGPTGCNIEGFFATLG
>RHO1_galGal                        MNGTEGQDFYVPMSNKTGVVRSPFEYPQY-YLAEPWKFSA LAAYMFMLILLGFPVNFLTLYVTIQHKKLRTPLNYILLNLVVADLFMVFGGFTTTMYTSMNGYFVFGVTGCYIEGFFATLG
>RHO1_anoCar                        MNGTEGQNFYVPMSNKTGVVRNPFEYPQY-YLADPWQFSA LAAYMFLLILLGFPINFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVLMGFTTTMYTSMNGYFIFGTVGCNIEGFFATLG
>RHO1_xenTro                        MNGTEGPNFYIPMSNKTGVVRSPFDYPQY-YLAEPWKYSA LAAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMHGYFIFGQTGCYIEGFFATLG
>RHO1_danRer                        MNGTEGPAFYVPMSNATGVVRSPYEYPQY-YLVAPWAYGF VAAYMFFLIITGFPVNFLTLYVTIEHKKLRTPLNYILLNLAIADLFMVFGGFTTTMYTSLHGYFVFGRLGCNLEGFFATLG
>RHO1_Raja                          MNGTEGENFYVPMSNKTGVVRSPFDYPQY-YLGEPWMFSA LAAYMFFLILTGLPVNFLTLFVTIQHKKLRQPLNYILLNLAVSDLFMVFGGFTTTIITSMNGYFIFGPAGCNFEGFFATLG
>RHO1_lamp1                         MNGTEGENFYIPFSNKTGLARSPFEYPQY-YLAEPWKYSV LAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAVANLFMVLFGFTLTMYSSMNGYFVFGPTMCNFEGFFATLG
>RHO1_lamp2                         MNGTEGQNFYIPFSNKTDVARSPFEYPQY-YLAEPWKFSA LAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAVSNLFMILFGFTTTMYTSMNGYFVFGPTMCSIEGFFATLG
>RHO1_lamp3                         MNGTEGDNFYVPFSNKTGLARSPYEYPQY-YLAEPWKYSA LAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG share second glyco, 2aa insert
>RHO2_galGal                        MNGTEGINFYVPMSNKTGVVRSPFEYPQY-YLAEPWKYRL VCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG share second glyco, 2aa insert
>RHO2_anoCar                        MNGTEGINFYVPLSNKTGLVRSPFEYPQY-YLAEPWKYKV VCCYIFFLIFTGLPINILTLLVTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFIFGPIGCAIEGFFATLG
>RHO2_Gekko                         MNGTEGINFYVPLSNKTGLVRSPFEYPQY-YLADPWKFKV LSFYMFFLIAAGMPLNGLTLFVTFQHKKLRQPLNYILVNLAAANLVTVCCGFTVTFYASWYAYFVFGPIGCAIEGFFATIG
>RHO2_Lat                           MNGTEGMNFYVPLSNRTGLVRSPFEYTQY-YLAEPWKFSV LCAYMFLLIILGFPINFLTLLVTFKHKKLRQPLNYILVNLAVASLFMVVFGFTVTFYSSLNGYFVLGPMGCAMEGFFATLG
>RHO2_Geo                           MNGTEGANFYIPFHNRTGVVRSPYEYPQY-YLADPWMYSA ISAYVFTLILIGFPVNFMTLFVTFKLKKLRQPLNFILVNLCVADLLMIMFGFTTTFYTAMNGYFVFGPTGCNIEGFFATLG
>SWS1_homSap                       MRKMS-EEEFYL-FKNIS--SVGPWDGPQY-HIAPVWAFYL QAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVA 2aa indel is above
>SWS1_macDom                          MSGDEEFYL-FKNIS--SVGPWDGPQY-HIAPAWAFHF QTVFMGFVFCAGTPLNAVVLVATLRYKKLRQPLNYILVNVSLCGFIFCIFAVFTVFISSSQGYFIFGRHVCAMEAFLGSVA
>SWS1_galGal                          MSSDDDFYL-FTNGS--VPGPWDGPQY-HIAPPWAFYL QTAFMGIVFAVGTPLNAVVLWVTVRYKRLRQPLNYILVNISASGFVSCVLSVFVVFVASARGYFVFGKRVCELEAFVGTHG
>SWS1_Taeniop                         MD-EEEFYL-FKNQS--SVGPWDGPQY-HIAPMWAFYL QTIFMGLVFVAGTPLNAIVLIVTIKYKKLRQPLNYILVNISVSGLMCCVFCIFTVFIASSQGYFVFGKHMCAFEGFAGATG
>SWS1_Gekko                           MSGEEDFYL-YANIS--SVGPFDGPQY-HIAPMWAFYF QTAFMGFVFFVGTPLNAIILFAIVKYKKLRQPLNYILVNISAAGFLFCVVAVFTVFISSSQGYFIFGKHICALEAFLGSLA
>SWS1_Utasta                          MSGEEDFYL-FENIS--SVGPWDGPQY-HIAPMWAFYF QTAFMGFVFFAGTPLNAIILIVTVKYKKLRQPLNYILVNISFAGFLFCVFSVFTVFLASSQGYFFFGRHICALEAFLGSVA
>SWS1_Xenopus                         MLEEEDFYL-FKNVS--NVSPFDGPQY-HIAPKWAFTL QAIFMGMVFLIGTPLNFIVLLVTIKYKKLRQPLNYILVNITVGGFLMCIFSIFPVFVSSSQGYFFFGRIACSIDAFVGTLT
>SWS1_Danio                           MD--AWAVQ-FGNAS--KVSPFEGEQY-HIAPKWAFYL QAAFMGFVFIVGTPMNGIVLFVTMKYKKLRQPLNYILVNISLAGFIFDTFSVSQVSVCAARGYYSLGYTLCSMEAAMGSIA
>SWS1_Oryzias                         MG--KYFYL-YENIS--KVGPYDGPQY-YLAPTWAFYL QAAFMGFVFFVGTPLNFVVLLATAKYKKLRVPLNYILVNITFAGFIFVTFSVSQVFLASVRGYYFFGQTLCALEAAVGAVA
>SWS1_Geotri                          MSGDEEFYL-FKNIS--KVGPWDGPQF-HIAPKWAFYL QAAFMGFVFICGTPLNAIVLVVTIKYKKLRQPLNYILVNISAAGLVFCLFSISTVFVASMQGYFFLGPTICALEAFFGSLA
>SWS2_ornAna             MHKTHRNLQNELPEDFFIPLPLDTDNIT--SLSPFLVPQT-HLGGSGIFMS LAAFMFLLITLGFPINLLTVICTIKYKKLRSHLNYILVNLAVSNMLVVCVGSATAFYSFAHMYFVLGPTACKIEGFAATLG
>SWS2_galGal             MH--PPRPTTDLPEDFYIPMALDAPNIT--ALSPFLVPQT-HLGSPGLFRA MAAFMFLLIALGVPINTLTIFCTARFRKLRSHLNYILVNLALANLLVILVGSTTACYSFSQMYFALGPTACKIEGFAATLG
>SWS2_Taenio              MPKPREMRDELPEDFYIPMSLETPNLT--ALSPFLVPQT-HLGSPGIFKA MAAFMFLLVLLGVPINALTVLCTAKYKKLRSHLNYILVNLAVANLLVVCVGSTTAFYSFSQMYFALGPLACKIEGFTATLG
>SWS2_Utasta             MHNSRPHSRDDLPEDFFIPMPLDVANIT--TLSPFLVPQT-HLGSPALFMG MAAFMFLLIILGVPINVLTIFCTFKYKKLRSHLNYILVNLAVSNLLVVCIGSTTAFYSFAQMYFSLGPTACKIEGFAATLG
>SWS2_Xenopu             MSKGRPDLRMEMPDEFYVPIPLETTNIS--SLSPFLVPQT-HLGTPGIFMS ISAFMLFTIIFGFPLNLLTIICTVKYKKLRSHLNYILVNLAVANLIVICFGSTTAFYSFSQMYFSLGTLACKIEGFTATLG
>SWS2_Danio                MKQQQQTPELFEDFHMPITLDVSNIS--AYSPFLVPQD-HLGHSGVFMG MSAFMLFLFIAGTAINVLTIVCTIQYKKLRSHLNYILVNLAISNLWVSVFGSSVAFYAFYKKYFVFGPIGCKIEGFTSTIG
>SWS2_Takifu                MRGVRQHEFQEDFYIPIPLDVDNIT--ALSPFLVPQD-HLGSPAVFYG MSAFMFFLFVAGTGINVLTIACTIQYKKLRSHLNYILVNLAFSNLLVTTVGSFTCFCCFFVRYMIVGPLGCKIEGFAATLG 
>SWS2_Geotri             MYQGKSTQVDDLPEDFYIPIALNVKNMS--ELSPFLVPQV-HLGDSFIFYG MSAFMLFLVLAGFPLNFLTVFVTIKYKKLRSHLNYILVNLAIANLIVVCCGSTLAFYSFMHKYFILGPLFCKMEGFTATLG
>LWS_ornAna      MTPAWNSGVYAARRRFEDEEDTTRTSVFVYTNSNNT---RDPFEGPNY-HIAPRWAYNV TSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFILGHPMCVLEGYTVSLC 1 aa indel
>LWS_galGal      MAAWEA--AFAARRR-HEEEDTTRDSVFTYTNSNNT---RGPFEGPNY-HIAPRWVYNL TSLWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGHPMCVVEGYTVSAC
>LWS_anoCar  MAGTVTEAWDVAVFAARRR-NDEDDTTRDSLFTYTNSNNT---RGPFEGPNY-HIAPRWVYNI TSVWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISGYFILGHPMCVLEGYTVSTC
>LWS_Lithoch     MAEEWGKQSFAARRY---HEDSTRGSAFAYTNSNNT---RDPFEGPNY-HIAPRWIYNL ATLWMFVVVVLSVFTNGLVLVATMKFKKLRHPLNWILVNLAIADLGETVFASTISVCNQFFGYFILGHPMCIFEGYVVSVC
>LWS_Gastero     MAEEWGKQAFAARRY---NEDTTRGSMFVYTNSNNT---KDPFEGPNY-HIAPRWVYNL STLWMFIVVALSVFTNGLVLVATAKFKKLQHPLNWILVNLAIADLGETVFASTISVCNQFFGYFILGHPMCVFEGYVVSVC
>LWS_Petrom      MTASWQGAMFAARRR-QDDEDTTMESLFRYTNENNT---KDPFEGPNY-HIAPRWVFNL TSVWMIIVVVLSLFSNGLVLVATVKFKKLRHPLNWIIVNLAIADILETIFASTISVCNQVYGYFILGHPMCVFEGYVVSTC
>LWS_lamprey     MTASWHGAVFAARRR-NDDEDTTKDSIFRYTNENNT---RDPFEGPNY-HIAPRWMFNL TSVWMIIVVVLSLFTNGLVLVATMKFKKLRHPLNWILVNLAIADILETIFASTISVCNQVFGYFILGHPMCVFEGYVVSTC
>LWS_Geotria     MAQSWERAMFAARRR--QDEDTTKGDLFRYTNENNT---RDPFEGPNY-HIAPRWMYNL TSFWMIIVVILSLFTNGLVLVATLKFKKLRHPLNWILVNLAIADIGETIFASTVSVVNQIFGYFILGHPLCVFEGFTVSVC
>PIN_galGal                             MSSNSSQAPPNGT---PGPFDGPQWPYQAPQSTYVG VAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLT P 1aa insert non-ancestral unless VAOP earlier
>PIN_utaSta                                 MVNEWSNAT---PGPFDGPQWPYLAPRSIYTS VAVLMGLVVVSAAFVNGLVIVVSIQYKKLRSPLNYILVNLAIADLLVTSFGSTLSFANNIYGFFVLGQTACEFEGFMVSLT these opsins are very limited frog to liz/bird
>PIN_pheMad                         MHVQMANASQASLKNGT---LSPFDGPQWPHRASRRVYTS LAALMGVVVLSASLANGLVIAVSVRFKRLRSPLNYILVNLATADLLVTFFGSIISFVNNAVGFFVFGKTACRFEGFMVSLT
>PIN_podSic                           MQASNASWVEVRNRT---PGPFEGPQWPYLAPQSTYIS VAVLMGLVVISATLVNGLVIVVSVQFKKLRSPLNYVLVNLAVADLLVTFFGSTISFVNNAQGFFIFGQATCEFEGFMVSLT
>PIN_xenTro                               MRAGNMSAYEA---PGPYDGPQWPHLAPRSTFLT VAAVMCMVVILAFFVNGLVIVVTLKYKKLRSPLNYILVNLAIANLLVTIFGSSVSFSNNVVGYFFMGKTMCEFEGFMVSLT the glyco is either not homologous or lost in frogs
>PIN_bufJap                               MHSANMSALET---PGPFEGPQWPHVAPRSTYLT VAVLMGMVVFLAFFVNGMVIVVSLKYKKLRSPLNYILVNLAVADILVTMFGSTVSFHNNIFGFFTLGKLVCELEGFVVSLT
>VAOP_galGal                       MDVFRALGNESLLSNSSGPARWDPFHHPLD-SIQP-WHFRL VAAVMFVVTSLSLAENLAVILVTFKFKQLRQPVNYVIVNLSVADFLVSLTGGTISFLANLKGYFYMGHWACVLEGFAVTFF no consistent glyco, much older than PIN
>VAOP_anoCar                        MAGLRREAENDSWLFDPSSSSAPFLQPLD-IIEP-WNFHL ISALMFVVTLFSLSENFTVILVTIKFKQLRQPLNYVIVNLSVADFLVSLIGGTISFSTNLKGYFYMGHWACVLEGFAVTFF losing all the invariant residues almost
>VAOP_xenTro                            MPTNVSLLATPENSTVWNPFTGPLK-TIEA-WNFHL LAALMFVVTSLSIAENFIVILVTAKFKQLRQPLNYIIVNLSVADFLVSVIGGTISIATNSRGYFYLGSWACVLEGFAVTFF
>VAOP_danRer                              MEASSAAVNAVSPAEDPFSAPLS-SIAP-WNYSV LAALMFVVTALSLSENFTVMLVTFRFQQLRQPLNYIIVNLSLADFLVSLTGGSISFLTNYHGYFFLGKWACVLEGFAVTFF
>VAOP_rutRut                              MELFPVAVNGVSHAEDPFSGPLT-FIAP-WNYKV LATLMFVVTAASLSENFAVMLVTFRFTQLRKPLNYIIVNLSLADFLVSLTGGTISFLTNYHGYFFLGKWACVLEGFAVTYF
>VAOP_Petro              MDALQESPPSHHSLPSALPSATGGNGTVATMHNPFERPLE-GIAP-WNFTM LAALMGTITALSLGENFAVIVVTARFRQLRQPLNYVLVNLAAADLLVSAIGGSVSFFTNIKGYFFLGVHACVLEGFAVTYF
>PPIN_anaCar                                    MDSLDTNTLSPNASTVRVVLMPRIGYTI IAIIMATSCTLSVILNTAVIAITIKYRQLRQPINYSLVNLAIADLGAALLGGSLNVETNAVGYYNLGRVGCVTEGFAMAFF
>PPIN_Xenop                                 MADEALLPPMMNVTNEEMHPGKVLMPRIGYTI LALIMAVFCAAALFLNVTVIVVTFKYRQLRHPINYSLVNLAIADLGVTVLGGALTVETNAVGYFNLGRVGCVIEGFAVAFF
>PPIN_Ictal                                 MASIILINFSETDTLHLGSVNDHIMPRIGYTI LSIIMALSSTFGIILNMVVIIVTVRYKQLRQPLNYALVNLAVADLGCPVFGGLLTAVTNAMGYFSLGRVGCVLEGFAVAFF
>PPIN_Danio                                        MESETSTAASGSIAE-VMPRMGYTI LAVIIGVFSVCGVILNVTVITVTLKYKQLRQPLNFALVNLAVADLGCAVFGGLPTVVTNAMGYFSLGRVGCVLEGFAVAFF
>PPIN_Oncor                                MDHQQLLPNLHGNISSSPGSVSEALLSRTGFTI LAVIIGVFSVSGVCMNVLVIMVTMRHRKLRQPLNYALVNLAVADLGCALFGGLPTMVTNAMGYFSMGRLGCVLEGFAVAFF
>PPINa_Ciona                  MDHDVTPTVDLTDGVPQCKDLNPYVLKGDGWVPQHISRANRSTYSF LCVYMTFVFLLSCSLNILVIVATLKNKVLRQPLNYIIVNLAVVDLLSGFVGGFISIAANGAGYFFWGKTMCQIEGYFVSNF
>PPINb_Ciona                MTTAETTTECYEKNPYIRNEMGWVPKHILIAERHIYTILAVYMTFIFL LAVYMTFIFLLAVSLNGFVIIATMKNKKLRQPLNYIIINLSIADFLSGLVGGFIGMISNSAGYFYFGKTVCILEGYIVSVA
>PPIN2_cioSa                               IPQNYSNGNPYATTDSGWVPEHIEIANRSTYSG LCVFMSFVFVLAVPLNLLVIVATYKNKVLRRPINYIIVNLAVADLTCSVVGGLLGVLNNGAGYYFLGKSVCIFEGYVMSVT
>PPIN_lamp                                         MENLTSLDLLPNGEVPLMPRYGFTI LAVIMAVFTIASLVLNSTVVIVTLRHRQLRHPLNFSLVNLAVADLGVTVFGASLVVETNAVGYFNLGRVGCVIEGFAVAFF 
>PARIE_Utast       ME-NDSSLATEL--------------------AEGAIVKPTIFPKAG-------YGV LAFLMFLNALFSIFNNSLVIAVTLKNPQLRNPINIFILNLSFSDLMMSLCGTTIVIATNYYGYFYLGRKFCIFQGFAVNYF 
>PARIE_Anole       ME--NESSLVLE--------------------AEGYIVRPTIFPRAG-------YGV LAFLMFINALFSLFNNFLVIAVTLKNPQLRNPINIFILNLSFSDLMMSICGTTIVIATNYHGYFYLGRRFCIFQGFAVNYF 
>PARIE_Xenop       MD-GNSTTPGI---------------------AVNLTVMPTIFPRSG-------YSI LSFLMFLNAVFSICNNAIVILVTLKHPQLRNPINIFILNLSFSDLMMALCGTTIVVSTNYHGYFYLGKQFCIFQGFAVNYF 
>ENCEPH_braBe       EY-GNNTTFAAWDFKRNGTGGEEEVEF-----------------FG-------YDA VAGVIAIIGVVGFVSNGAVVVLFLKFPQLRTPFNLLLLNMAVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 
>ENCEPH_homS       MYSGNRS--------GGHGYWDGGGAAGAEG------PAPAGTLSPAPLFSPGTYER LALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 
>ENCEPH_monD       MYSDNSS------DDGGGGYWGSGRAGGASGTGVTGEPGPEGSPRQAPLFSPGTYEL LALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 
>ENCEPH_galG       MHSGNGT---------------------GATSRPQLAAAGHEVPGERPLFSAGTYEL LALLIATIGTLGVCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVCGVSLTFMSCLRSRWVWDAAGCVWDGFSNSLF 
>ENCEPH_anoC       MFSANGT---------RSGAGSDLEPGPGQQQQQREASEEEERGAGLSPFSAGTYEL LALLVAAIGLLGLCNNLLVLVLYAKFKRLRTPTHLFLVNISLSDLLVSLFGVSFTFGSCLRHRWVWDAAGCVWDGFSNSLF 
>ENCEPH_xenT       MPVTNGS-----------------------------HNNSISWLHSKDMFTEDTYHF LALIVATVGFLGLVNNLLVLILYCKFKRLQTPTNLLFFNTSLCHFVFSLLAITFTFMSCVRGSWAFSVEMCVFHGFSKNLL 
>ENCEPH_braB       MPLYNTSSGPTQGLPWDTPYSQDPIWNDSSPSNSSEDAVVDQGRGELQDFSDAGYTA IATGLALIGLVGSMNNFVVILLIGCHRQLRTPFNLLLLNVSVADLLVSVCGNTLSFASAVQHRWLWGRPGCVWYGFANSLF 
>ENCEPH_braF       MALYNNTSSPSQDLLWDAPYSQGHIW-DNSSASNSSEDVMDQGKVELQDFSDAGYTA IATCLALIGFVGFTNNFVVILLIGCHRQLRTPFNLLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANSLF 
>ENCEPH2_Api                                              MEHVIYEDQVSPVMYIGA AIALGFIGFFGFTANLLVAIVIVKDAQILWTPVNVILFNLVFGDFLVSIFGNPVAMVSAATGGWYWGYKMCLWYAWFMSTL 
>ENCEPH1_Ano                                      MYDVTDAAAINSDHQELMAPWAYNGA AVTLFFIGFFGFFLNIFVIALMYKDVQ-LWTPMNIILFNLVCSDFSVSIIGNPLTLTSAISHRWLYGKSICVAYGFFMSLL 
>ENCEPH2_Ano                                     MNDAPNDVAASAVDYEDLMAPWAYNAS AVTLFFIGFFGFFLNLFVIALMCKDMQ-LWTPMNIILFNLVCSDFSVSIIGNPLTLTSAISHRWIFGRTLCVAYGFFMSLL 
>CILL2_Platyr                        MDDLGFLGNSSVNYTVPLLQEDPLLLRILYFGPTSYVIT AIYLCIVGVIGTLSNGVIMYLYFKDKSLRSPMNLLFVNLAMSDFTVAFFGAMFQFGLTCTRKYMSPGMALCDFYGFITFLG 
>CILL1_Platyr            MDGENLTIPNPVTELMDTPINSTYFQNLNAETDGGNHYIYNAFTATDYNIC AAYLFFIACLGVSLNVLVLVLFIKDRKLRSPNNFLYVSLALGDLLVAVFGTAFKFIITARKTLLREEDGFCKWYGFITYLG
                                     !!!    ***   !!!     **  ***   * *  *
>RHO1_homSap                        MNGTEGPNFYVPFSNATGVVRSPFEYPQY-YLAEPWQFSM LAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG


Here's the distal alignment of the opsins and a blurb on how the gene classifier can be used:

>RHO1_homSap   RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE AAAQQQESATTQKAEK----EVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ FRNCMLTTIC CGKNPLG DDEASATVS  KTE     TSQVAPA
>RHO1_monDom   RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGQLVFTVKE AAAQQQESATTQKAEK----EVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTIPAFFAKSSSVYNPVIYIMMNKQ FRTCMITTLC CGKNPLG DDEASATAS  KTE     TSQVAPA
>RHO1_ornAna   RYIPEGMQCSCGIDYYTLRPEVNNESFVIYMFVVHFTIPMTIIFFCYGRLVFTVKE AAAQQQESATTQKAEK----EVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTVPAFFAKSSAIYNPVIYIMMNKQ FRNCMLTTIC CGKNPLG DDEASATAS  KTEQSSVSTSQVSPA
>RHO1_galGal   RYIPEGMQCSCGIDYYTLKPEINNESFVIYMFVVHFMIPLAVIFFCYGNLVCTVKE AAAQQQESATTQKAEK----EVTRMVIIMVIAFLICWVPYASVAFYIFTNQGSDFGPIFMTIPAFFAKSSAIYNPVIYIVMNKQ FRNCMITTLC CGKNPLG DEDTSAG    KTETSSVSTSQVSPA
>RHO1_anoCar   RYIPEGMQCSCGVDYYTPTPEVHNESFVIYMFLVHFVTPLTIIFFCYGRLVCTVKA AAAQQQESATTQKAER----EVTRMVVIMVISFLVCWVPYASVAFYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQ FRNCMIMTLC CGKNPLG DEDTSAGT   KTETSTVSTSQVSPA
>RHO1_xenTro   RYIPEGMQCSCGVDYYTLKPEVNNESFVVYMFIVHFTIPLCVIFFCYGRLLCTVKE AAAQQQESATTQKAEK----EVTRMVVMMVIFFLICWVPYAYVAFYIFTHQGSDFGPVFMTVPAFFAKSSAIYNPVIYIVLNKQ FRNCLITTLC CGKNPFG DEEGSSAASS KTEASSVSSSQVSPA
>RHO1_danRer   RYIPEGMQCSCGVDYYTRTPGVNNESFVIYMFIVHFFIPLIVIFFCYGRLVCTVKE AARQQQESETTQRAER----EVTRMVIIMVIAFLICWLPYAGVAWYIFTHQGSEFGPVFMTLPAFFAKTSAVYNPCIYICMNKQ FRHCMITTLC CGKNPFE EEEGASTTAS KTEASSVSSSSVSPA
>RHO1_Raja     RYIPEGLQCSCGVDYYTMKPEVNNESFVIYMFVVHFTIPLIVIFFCYGRLVCTVKE AAAQQQESESTQRAER----EVTRMVIIMVVAFLICWVPYASVAFYIFINQGCDFTPFFMTVPAFFAKSSAVYNPLIYILMNKQ FRNCMITTIC LGKNPFE EEESTSASAS KTEASSVSSSQVAPA
>RHO1_lamprey1 RYLPEGMQCSCGPDYYTLNPNFNNESFVIYMFLVHFIIPFIVIFFCYGRLLCTVKE AAAAQQESASTQKAEK----EVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTVPAFFAKTSALYNPIIYILMNKQ FRNCMITTLC CGKNPLG DEDSGASTS  KTEVSSVSTSQVSPA
>RHO1_lamprey2 RYLPEGMQCSCGPDYYTMNPTYNNESFVIYMFIVHFTIPFVIIFFSYGRLLCTVKE AAAAQQESASTQKAEK----EVTRMVVLMVVGFLVCWVPYASVAFYIFTNQGSDFGATFMTLPAFFAKSSALYNPVIYILMNKQ FRNCMITTLC CGKNPLG DDDSGASTS  KTEVSSVSTSQVAPA
>RHO1_lamprey3 RYIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKE AAAAQQESASTQKAEK----EVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSALYNPVIYILMNKQ FRNCMITTLC CGKNPLG DDESGASTS  KTEVSSVSTSQVSPA
>RHO2_galGal   RYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVRE AAAQQQESATTQKAEK----EVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSLYNPIIYVLMNKQ FRNCMITTIC CGKNPFG DEDVSSTVSQSKTEVSSVSSSQVSPA
>RHO2_anoCar   RYIPEGMQCSCGPDYYTLNPDYHNESYVLYMFGVHFVIPVVVIFFSYGRLICKVRE AAAQQQESASTQKAER----EVTRMVILMVLGFLLAWTPYAMVAFWIFTNKGVDFSATLMSVPAFFSKSSSLYNPIIYVLMNKQ FRNCMITTIC CGKNPFG DEDVSSSVSQSKTEVSSVSSSQVSPA
>RHO2_Gekko    RFIPEGMQCSCGPDYYTLNPDFHNESYVIYMFIVHFTVPMVVIFFSYGRLVCKVRE AAAQQQESATTQKAEK----EVTRMVILMVLGFLLAWTPYAATAIWIFTNRGAAFSVTFMTIPAFFSKSSSIYNPIIYVLLNKQ FRNCMVTTIC CGKNPFG DEDVSSSVSQSKTEVSSVSSSQVAPA
>RHO2_Latime   RYIPEGLQCSCGPDYYTLNPDFHNESYVMYLFLVHFLLPIIIIFFTYGRLICKVKE AAAQQQESASTQKAEK----EVTRMVILMVIGFLTAWVPYASAAFWIFCNRGAEFTATLMTVPAFFSKSSCLFNPIIYVLLNKQ FRNCMITTLC CGKNPLG DDDTSSAVSQSKTDVSSVSSSQVSPA
>RHO2_Geot     RYIPEGMQCSCGPDYYTLNPKYYNESYVIYLFLVHFLLPVTIIFFTYGRLICTVKE AAAQQQESASTQKAER----EVTRMVIIMVVGFLVCWVPYASFAFYLFMNKGILFSATAMTVPAFFSKSSVLYNPIIYVLLNKQ FRTCMVTTLF CGKNPFG EDDSSMVSTS KTEVSSVSSSQVSPS
>SWS1_homSap   RFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKA VAAQQQESATTQKAER----EVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNPIIYCFMNKQ FQACIMKMV  CGKAMTDESDTCSSQ    KTEVSTVSSTQVGPN
>SWS1_macDom   RFIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIMPLFLICFSYSQLLRALRA VAAQQQESATTQKAER----EVSRMVVMMVGSFCLCYVPYAALAMYMVNNQNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ FHACIMEMV  CRKPMTDDSDVSSSQ    KTEVSAVSSSQVGPT
>SWS1_galGal   RYMPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLIIFSYSQLLSALRA VAAQQQESATTQKAER----EVSRMVVVMVGSFCLCYVPYAALAMYMVNNRDHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ FRACIMETV  CGKPLTDDSDASTSAQ   RTEVSSVSSSQVGPT
>SWS1_Taeni    RYIPEGLQCSCGPDWYTVGTKYKSEYYTWFLFIFCFIVPLSLIIFSYSQLLSALRA VAAQQQESATTQKAER----EVSRMVVVMVGSFCMCYVPYAALAMYMVNNREHGIDLRLVTIPAFFSKSSCVYNPIIYCFMNKQ FRACIMETV  CGRPMTDDSEVSSSAQ   RTEVSSVSSSQVGPS
>SWS1_Gekko    RFIPEGLQCSCGPDWYTVGTKYYSEYYTWFLFVLCFIVPLSIIVFSYSQLLSALRA VAAQQQESATTQKAER----EVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNHGIDLRMVTIPAFFSKSSCVYNPIIYCFMNKQ FRGCILEMV  CGKTMAEESEVSSASQ   KTEVSSVSSSQVGPS
>SWS1_Uta      RFIPEGLQCSCGPDWYTVGTKYKSEYYTWFLFIFCFIVPLTLIIFSYSQLLGALRA VAAQQQESATTQKAER----EVSRMVVVMVGSFCLCYVPYAALAMYMVNNRDHGIDLRLVTIPAFFSKSACVYNPIIYCFMNKQ FRACIMETV  CGKPMTDESDVSSSAQ   KTEVSSVSSSQVSPS
>SWS1_Xenop    RYMPEGLQCSCGPDWYTVGTKYRSEYYTWFIFIFCFVIPLSLICFSYGRLLGALRA VAAQQQESASTQKAER----EVSRMVIFMVGSFCLCYVPYAAMAMYMVTNRNHGLDLRLVTIPAFFSKSSCVYNPIIYSFMNKQ FRGCIMETV  CGRPMSDDSSVSSTSQ   RTEVSTVSSSQVSPA
>SWS1_Danio    RYIPEGLGCSCGPDWYTNCEEFSCASYSKFLLVTCFICPITIIIFSYSQLLGALRA VAAQQAESASTQKAEK----EVSRMIIVMVASFVTCYGPYALTAQYYAYSQDENKDYRLVTIPAFFSKSSCVYNPLIYAFMNKQ FNACIMETV  FGKKIDESSEVSS      KTETSSVSA
>SWS1_Oryzia   RYIPEGLQCSCGPDWYTVGTKYKSEYYTYFLFVFCFVVPLSIIIFSYGSLLGTLRA VAAQQQESASTQKAER----EVSRMVIMMVASFCTCYVPYAALAVYMVTNRDHNIDLRFVTVPAFFSKASCVYNPLIYSFMNKQ FNGCIMEMV  FGKKMEEASEVSS      KTEVSTDS
>SWS1_Geotri   RYIPEGLQCSCGPDWYTVGTKYKSEYYTYFLFVFCFVVPLSIIIFSYGSLLGTLRA VAAQQQESASTQKAER----EVSRMVIMMVASFCTCYVPYAALAVYMVTNRDHNIDLRFVTVPAFFSKASCVYNPLIYSFMNKQ FRACILETV  CGKPITDESETSSS     RTEVSSVSTTQMIPG
>SWS2_ornAna   RYIPEGLQCSCGPDWYTTNNKWNNESYVIFLFSFCFGVPLSIIIFSYGRLLLTLRA VAKQQEQSATTQKAER----EVTKMVIVMVLGFLVCWLPYASFSLWVVTNRGQVFDLRMASIPSVFSKASTIYNPIIYVFMNKQ FRSCMLKLVF CGKSPFGDEDEISGSS   QATQVSSVSSSQVSPA
>SWS2_galGal   RYIPEGLQCSCGPDWYTTDNKWHNESYVLFLFTFCFGVPLAIIVFSYGRLLITLRA VARQQEQSATTQKADR----EVTKMVVVMVLGFLVCWAPYTAFALWVVTHRGRSFEVGLASIPSVFSKSSTVYNPVIYVLMNKQ FRSCMLKLLF CGRSPFGDDEDVSGSS   QATQVSSVSSSHVAPA
>SWS2_Taeni    RYIPEGLQCSCGPDWYTTDNKWNNESYVIFLFCFCFGFPLTVIVFSYGRLLLTLRA VAKQQEQSASTQKAER----EVTKMVVVMVLGFLVCWLPYCSFALWVVTHRGHPFDLGLASIPSVFSKASTVYNPIIYVFMNKQ FRSCMLKLVF CGRSPFGDEDDVSGSS   QATQVSSVSSSQVSPA
>SWS2_Uta      RYIPEGLQCSCGPDWYTTNNKWNNESYVLFLFSFCFGVPLSVIIFSYGRLLLTLRA VAKQQEQSATTQKAER----EVTKMVVVMVMGFLVCWLPYASFALWVVTHRGEPFDVRLATIPSVFSKASSVYNPVIYVFMNKQ FRSCMLKLVF CGKSPFGDEDDVSGSS   QTTQVSSVSSSQVSPA
>SWS2_Xeno     RYIPEGLQCSCGPDWYTVNNKWNNESYVLFLFCFCFGFPLAIIVFSYGRLLLALHA VAKQQEQSATTQKAER----EVTRMVIVMVVGFLVCWLPYASFALWAVTHRGELFDLRMSSVPSVFSKASTVYNPFIYIFMNRQ FRSCMMKMIF CGKNPLGDDEETSVSG    STQVSSVSSSQIAPS
>SWS2_Danio    RYIPEGLQCSCGPDWYTTNNKFNNESYVMFLFCFCFAVPFSTIVFCYGQLLITLKL AAKAQADSASTQKAER----EVTKMVVVMVFGFLICWGPYAIFAIWVVSNRGAPFDLRLATIPSCLCKASTVYNPVIYVLMNKQ FRSCMMKMVF NKNIEEDEASSSS      QVTQVSSVAPEK
>SWS2_Takif    RYIPEGFQCSCGPDWYTTGNKYNNESYVWFIFGFGFAVPLFVIVFCYSQLLVMLKS AAKAQAESASTQKAER----EVTRMVVVMILGFLVCWLPYASFALWVVNNRGTPFDLRLATIPACFSKASTVYNPIIYVVLNKQ FRSCMKKMLG MSGGDDEESSS          QSVTEVSKVSPS
>SWS2_Geotria  RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFIFCFGTPFTIIIVSYSKLILTLRA AAAQQQESASTQKAEK----EVSRMVVIMVGGFLVCWLPYASLALWIVFNRGSPFDLRLATIPSVFSKASTVYNPVIYIFLNKQ FRSCMMKTIF CGKNPLGDDEDATSTTT    QVSSVSTSQVAPA
>LWS_ornAna    RYWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIVLCYLQVWLAIRA VAKQQKESESTQKAEK----EVSRMVVVMILAYCFCWGPYTIFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ FRNCIMQL   FGKKVDDGSELSSTS    RTEVSSVSS  VSPA
>LWS_galGal    RYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVSLAIRA VAAQQKESESTQKAEK----EVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ FRNCILQL   FGKKVDDGSEVSTS     RTEVSSVSNSSVSPA
>LWS_anoCar    RYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILLCYLQVWLAIRA VAAQQKESESTQKAEK----EVSRMVVVMIIAYCFCWGPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ FRNCIMQL   FGKKVDDGSELSSTS    RTEVSSVSNSSVSPA
>LWS_Lithoch   RYWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMLTCCIFPLAIIILCYLAVWMAIRA VAMQQKESESTQKAER----EVSRMVVVMIVAYCVCWGPYTFFACFAAANPGYAFHPLAAAMPAYFAKSATIYNPIIYVFMNRQ FRTCIMQL   FGKQVDDGSEVSTS     KTEV     SSVAPA
>LWS_Gastero   RYWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMITCCLIPLAIIILCYLAVWLAIRA VAMQQKESESTQKAER----DVSRMVVVMIVAYIVCWGPYTTFACFAAANPGYAFHPLAAAMPAYFAKSATIYNPVIYVFMNRQ FRSCIMQL   FGKEVDDGSEVSTs     KTEV     SSVAPA
>LWS_Petromy   RYWPHGLKTSCGPDVFSGSTDPGVQSYMVVLMITCCFLPLSIIILCYLQVWLAIHS VAQQQKESETTQKAER----DVSRMVVVMILAYVFCWGPYTFFACFAAANPGYSFHPIAAALPAYFAKGATIYNPIIYVFMNRQ FRNCILQL   FGKKVDDGSEVSSSS    RTEVSSVSNSSVSPA
>LWS_lamprey   RYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFLPLSVIILCYLQVWLAIHS VAQQQKESETTQKAER----DVSRMVVVMILAYIFCWGPYTFFACYAAANPGYAFHPLTAALPAYFAKSATIYNPVIYVFMNRQ FRNCIMQL   FGKKVDDGSEVSSAS    RTEVSSVSNSSISPA
>LWS_Geotria   RYWPHGLKTSCGPDVFSGSTDPGVQSYMVVLMITCCFIPLALIIICYLQVWLAIHT VAQQQKESETTQKAER----DVSRMVVVMIFAYIFCWGPYTFFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ FRNCIMQL   FGKKVDDGSEVSSSA    RTEVSSVSNSSVSPA
>PIN_galGal    SYVPEGLRTSCGPNWYTGGSNNN--SYILSLFVTCFVLPLSLILFSYTNLLLTLRA AAAQQKEADTTQRAER----EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVFMNKQ FQSCLLEMLC CGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
>PIN_Uta sta   SYVPEGLRTSCGPNWYTGGSGNN--SYIMALFVTCFALPLGMIIFSYASLLLTLRA VATQQKEVETTQQAEK----EVTRRVIAMVMAFLVCWLPYASFAMVVATNKDLVIQPALASLPSYFSKTATVYNPIIYVFMNKQ FRSCLLSTMS CGHRPRGAQETTPAMISIPQGPTSALQGSRNKVTPSA
>PIN_Phelsuma  SYVPEGLGTSCGPNWYMGGTNNN--SYIVALFVTCFALPLSMILFSYANLLLTLRA VAAQQKEQETTQRAEK----EVTRMVITMVMAFLVCWLPYATFAMVVATTKDLSIQPGLASLPSYFSKTATVYNPIIYVFMNKQ FRSCLLNTVS CGRIPQTMPGTPATTAVRGGFVLTSEGRGNKVASTEL
>PIN_Podarcis  SYVPEGLRTSCGPNWYSGGSSNN--SYIMTLFVTCFAMPLSTILFSYANLLMTLRT VAAQQKEQETTQRAER----EVTRMVVAMVAAFLVCWLPYASFAMVVATHKDLAIRPALASLPSYFSKTATVYNPIIYVFMNKQ FRSCLLYKMS CGHRALSSQDTTPAGISLPGRLTTSASKGSRNQVSPS
>PIN_xenTro    SYVPEGLRTSCGPNWYTGGTNNN--SYIMALFLTCFIMPLSTIIFSYSNLLMALRA VAAQQKDSETTQRAEK----EVTRMVIAMVLAFLICWLPYASFAVVVAVNKDVVIEPTVASLPSYFSKTATVYNPIIYVFMNKQ FRNCLMTLLC CGRSFGDDETSSASGRTDVTSVSEAGGNKVTPA
>PIN_Bufo      SYVPEGLGTSCGPNWYTGGTNNN--SYILALFTTCFMMPLTTIIFSYSNLLLALRA VAAQQKESETTQRAER----EVTRMVIAMVLAFLICWLPYAVFAIVMASNKNVVIDPTLASMPSYFSKTATVYNPVIYVFMNKQ FRDCLTKLLC CGRNPFGEDETSTTSGRTDVTSVSEGGGNKVTPA
>CILL2_Platyn  SYRPEGLGTWCSISWQDRSMNTM--SYVTAVFLGCYFFPVSIIIFCYFNVWRKVKE AADAQGAGTAGKAEKS-----IFRMSVIMVTCYLTAWTPYAIVCLIASYGPPNGLPIYAEVLPSLFAKSSQVYNPIIYVLMNKP 
>ENCEPH_braBel SYQFEGHSVGCSVNWVKHNVNNV--SYIITLMVTCFFVPMVVVCWSYACIWRTVRM SAEMKSEFGNPQNTGR----LVTTMVVVMIVCFLVCWTPYTVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ FREFLLARLRTFCCRQPRMLRVTPMDDNAHARLVGEGPSHAQQVIPSEEN
>ENCEPH_braFlo SYQFEGHNVGCSVNWVQHNPDNV--SYIVTLMVTCFFVPMVVVCWSYAWIWRTVRM SSEAKPECGNSQNAGR----LVTTMVVVMIICFLVCWTPYAVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ FREFLLARLQRVCCRQQAVPRVTPMDDNVHVRLGGEGPSQSQQFLPAGEN
>VAOP_galGal   SYTTSKIGTTCEPNWYSGAYNDR--SYIIAFFTTCFIVPLLVILVSYGKLLQKLRK VSNTQGRLRTARKPER----QVTRMVVVMIIAFLICWMPYAVFSILATAYPSIELDPHLAAIPAFFSKTATVYNPIIYVFMNKQ FRMCLIQMFK CSAIETAESNMNPTSERATLTQDKRDSQLSVMAVRST
>VAOP_anoCar   SYTTSKIGTTCEPNWYSGDYNDH--TFIITFFTTCFILPLLVILVSYGKLMRKLRK VSDTQGRLGTTRKPER----QVTGMVVIMILAFLICWSPYAAFSILVTACPSIELDPRLAAIPAFFSKTATVYNPVIYVFMNNQ FRKCLVQLFQ CSSQETMDANVNPISEKDTLTHTKHCGEMSTVAAHVI
>VAOP_xenTro   SYTTSKIGTTCEPNWYSGEMRDH--TYIITFLTTCFVFPLLVIFMSYGKLMRKLRK VSDTQGRLGSTRKPEK----EVTRMVVIMILAFLICWTPYAAFSILITAHPTIDLDPRLAAIPAFFAKTASMYNPIIYVYMNKQ FRRCLYQMFN INDPEAKESNLNPTSERGVLTRNNNGGEMLAIATHIT
>VAOP_Danio    SYTVSRIGTTCEPNWYSGNFHDH--TFIITLFSTCFIFPLGVIIVCYCKLIRKLRK VSNTHGRLGNARKPER----QVTRMVVVMIVAFMVAWTPYAAFSIIITAHPSMHVDPRLAAIPAFVAKTAAVYNPIIYVFMNKQ FRKCLVQLLS CSKVTVVEGNNNQTTERAGMTSGSNTGEMSAIAARVS
>VAOP_Ruti     SYTVSKIGTTCEPNWYSGNFHDH--TFIIAFFITCFILPLGVIVVCYCKLIKKLRK VSNTHGRLGNARKPER----QVTRMVVVMIVAFMVAWTPYAAFSIVVTAHPSIHLDPRLAAAPAFFSKTAAVYNPVIYVFMNKQ FRKCLVQLLR CRDVTIIEGNINQTSERQGMTNESHTGEMSTIASRIP
>VAOP_Petrom   SYRPSMIGTTCEPNWYSGELHDH--TFILMFFSTCFIFPLAVIFFSYGKLIQKLKK ASETQRGLESTRRAEQ----QVTRMVVVMILAFLVCWMPYATFSIVVTACPTIHLDPLLAAVPAFFSKTATVYNPVIYIFMNKQ FRDCFVQVLP CKGLKKVSATQTAGAQDTEHTASVNTQSPGNRHNIAL
>PPIN_anaCar   GYQMEGVMTSCAPDWANSDPINV--SYIICYFLFCFTIPFITILASYGYLIWTLRQ VAKVGLAQRGSTTKAEA---QVSRMVIVMVMAFLICWLPYATFALVVVGNPQIYINPIIATIPMYMAKSSTFYNPIIYIFMNKQ FRDCLVRCLL CGRNPCASEQTDEDDLEVSTIAPAPSSRRGKVAPV
>PPIN_Xeno     SYELEGVMTSCAPNWYSADPVNM--SYIVCYFSFCFAIPFLIIVGSYGYLMWTLRQ VAKLGVAEGGTTSKAEV---QVSRMVIVMILAFLVCWLPYAAFAMTVVANPGMHIDPIIATVPMYLTKTSTVYNPIIYIFMNKQ FQECVIPFLF CGRNPWAAEKSSSMETSISVTSGTPTKRGQVAPA
>PPIN_Icta     SYQLEGVMTSCAPNWYRRDPVNV--SYILCYFMLCFALPFATIIFSYMHLLHTLWQ VAKLQVADSGSTAKVEV---QVARMVVIMVMAFLLTWLPYAAFALTVIIDSNIYINPVIGTIPAYLAKSSTVFNPIIYIFMNRQ FRDYALPCLL CGKNPWAAKEGRDSDTNTLTTTVSKNTSVSPL
>PPIN_Danio    RLQLEGVRTSCAPDWYSRDLANV--SFIVCYFLLCFALPFSVIVYSYTRLLWTLRQ VSRLQVCEGGSAARAEA---QVSCMVVVMILAFLLTWLPYASFALCVILIPELYIDPVIATVPMYLTKSSTVFNPIIYIFMNRQ FRDRALPFLL CGRNPWAAEAEEEEEETTVSSVSRSTSVSPA
>PPIN_Oncorhy  SFELEGVRTSCSPNWYSREPGNM--SYIILYFLLCFAIPFSIIMVSYARILFTLHQ VSKLKVLEGNSTTRVEI---QVVRMVVVMVMAFLLSWLPYAAFALSVILDPSLHINPLIATVPMYLAKSSTVYNPIIYVFMNRQ FRDCAVPFLL CGLNPWASEPVGSEADTALSSVSKNPRVSPQs
>PPIN_lamp     SYELEGVRTSCAPDWYSRDPANV--SYITSYFAFCFAIPFLVIVVAYGRLMWTLHQ VAKLGMGESGSTAKAEA---QVSRMVVVMVVAFLVCWLPYALFAMIVVTKPDVYIDPVIATLPMYLTKTSTVYNPIIYIFMNRQ FRDCAVPFLL CGRNPWAEPSSESATAASTSATSVTLASAPGQVSPS
>PARIE_Uta     SYGPEGVQTSCSIGWEERSWSNY--SYLIVYFLSCFFIPVLIIGFSYGNVIRSLHG LNKKVEQLGGKSSPEEEF--RAVIMVLVMVVAFLICWLPYTVFALIVVFNPALNISPLAATIPTYLSKTSPVYNPIIYIFLNKQ FRDCAVEFIT CGQVVLTSPEEDISTSAIPVEGKGPCKINQVTPV
>PARIE_Anole   SYGPEGVQTSCSIGWEERSWNNY--SYLIVYFLSCFFIPVLIIGFSYGNVIRSLHG LNKKVEQLGGKSNPEEEF--RAVIMVLVMVVAFLICWLPYTLFALTVVFNPALNISPLAATIPTYLSKTSPVYNPIIYIFLNKE FRECAVEFIT CGKVVLTSPEEDISTSAISDEGIAPCKINQVTPV
>PARIE_Xenop   SYGPEGVQTSCSIGWEERSWSNY--SYIISYFLTCFIIPVGIIGFSYGSILRSLHQ LNRKIEQQGGKTNPREEK--RVVIMVLFMVLAFLICWLPYTVFALIVVINPQLYISPLAATLPTYFAKTSPVYNPIIYIFLNKQ FRTYAVQCLT CGHINLDSLEEDTESVSAQAENMLTPKTNQVAPA
>ENCEPH_braBel SYQLEGPKIGCSVAWEEHSWSNT--SYIVVLFITCLFAPLLIIVYSYYRLWHKVKQ GSRNLPAAMRKSSQKEQ---KIAMMVIVMITCFMVCWLPYGAMALVVTFGGERLISHTAAVVPSLLAKSSTCYNPVVYFAMNSQ FRRYFQDLLC CGRRLFDVSQSVVTGNTAMPRNNSQGFRKDDSDQKQD
>ENCEPH_homSap RYILDVHGLGCTVDWKSKDANDS--SFVLFLFLGCLVVPLGVIAHCYGHILYSIRM LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK FRRCLLQLLC FRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVT
>ENCEPH_monDom RYTLEIHGLGCSVDWKSKDPNDS--SFVIFLFFGCLMLPVGVMAYCYGHILYAIRM LRCVEELQTIQVIKILRYEKKVAKMCFLMIAIFLFCWMPYAVICLLVANGYGSLVTPTVAIIASLFAKSSTAYNPIIYIFMSRK FRRCLLQLLC FRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVT
>ENCEPH_galGal RYTLEIHGLGCSMDWKSKDPNDT--SFVLLFFLGCLVAPVVIMAYCYGHILYAVRM LRCVEDFQTSQVIKLLKYEKKVAKMCFLMISTFLICWMPYAVVSLLVTYGYSNLVTPTVAIIPSFFAKSSTAYNPVIYIFMSRK FRQCLLQLLC FRLMRFQRIMKEPSGAGNVKPIRPIVMSQKVGDRPKKKVT
>ENCEPH_anoCar HYTLEIHGLGCSVDWQSKEPSDS--SFVLFFFLGCLAAPVGIMAYCYGHILHAIRM LRCVEDLQSIQVIKILRYEKKVAKMCFLMVTTFLICWMPYAVVSLLIAYGYGHLITPTVAIIPSFFAKSSTAYNPVIYIFMSRK FRRCLVQLFC VQFLRFKRTLKEQPAIESNKPIRPIVMSQKVGDRPKKKVT
>ENCEPH_xenTro LYTFETHKLDCSFEWTATDPKDT--AFVLLFFLACITLPLSIMAYCYGYILYEIQK LRSVKNIQNFQEITILDYEIKMAKMCLLMMLTFLIGWMPYTILSLLVTSGYSKFITPTITVMPSLLAIASAAYNPVIHIFTIKK FRQCLVQLLP PINFHPPINPPINNFWRLLKNLNGRLAMKKVKPVLGKGRS
>ENCEPH1_Anoph AYVNEAANISCSVNWESQTANAT--SYIIFLFIFGLILPLAVIIYSYINIVLEMRK NSARVGRVNRAERRVT-------SMVAVMIVAFMVAWTPYAIFALIEQFGPPELIGPGLAVLPALVAKSSICYNPIIYVGMNTQ FRAAFWRIRR SNGVAGQPDSNNTNNSNRDKESARHTAKEGL
>ENCEPH2_Anoph AYVQEAANISCSVNWESQTKNAT--TYIIFLFVFGLVVPLIVIVYSYTNIIVNMRE NSARVGRINRAEQRVT-------SMVAVMIVAFMVAWTPYAIFALIEQFGPPELIGPGLAVLPALVAKSSICYNPIIYVGMNTQ FRAAFSRVRN KGQQAAADQNTTTMQRELTKSSRDMVECSF
>ENCEPH2_Apis  SYGPEAGNVSCSVSWEVHDPVTNSDTYIGFLFVLGLIVPVFTIVSSYAAIVLTLKK VRKRAGASGRREAKIT-------KMVALMITAFLLAWSPYAALAIAAQYFNAKPSATV-AVLPALLAKSSICYNPIIYAGLNNQ FSRFLKKIFD ARGSRTAVPDSQHTALTALNRQEQRK
>CILL1_Platyn  HYIPEGLATWCSIDWLSDETSDK--SYVFAIFIFCFLVPVLIIVVSYGLIYDKVRK VAKTGGSVAKAEREVL-------RMTLLMVSLFMLAWSPYAVICMLASFGPKDLLHPVATVIPAMFAKSSTMYNPLIYVFMNKQ FRRSLKVLLG MGVEDLNSESERATGGTATNQVAAT
>PER_homSap    SYAPDPTGATCTINWRKNDRSFV--SYTMTVIAINFIVPLTVMFYCYYHVTLSIKH HTTSDCTESLNRDWSD--QIDVTKMSVIMICMFLVAWSPYSIVCLWASFGDPKKIPPPMAIIAPLFAKSSTFYNPCIYVVANKK FRRAMLAMFK CQTHQTMPVTSILPMDVSQNPLASGRI
>PERa_Bran     EYALEPSGTACTINFQKNDSLYI--SYVTSCFVLGFVVPLAVMAFCYWQASCFVSK VLKGDIAGDLTFPVAAN.QNHFSKMCLAMVAAFVVAWTPYSVLFLFAAFWNPADIPAWLTLLPPLIAKSSALYNPIIYIIANRR FRNAICSMMK GQDPDVEDDEHADEHRVRSIEDNDKEIISMVNLNMTV
>PERc_Bran     YTYETPMQITCSLDWNVQHPGEK--AYIAAVLVIVYVLQVLIMCFCYFNIIFKSAN LKFAALASEKTKMAAKKDTWKTSVMCLTMVVSFLIAWTPYAVSSTWDILSAE-DLPIIATILPSLFAKSSCMMNPIIYACCNTK FRQAAVKSFR KLCGMCKQKVPLSTPQVVLAMQRNTEFTSTVEPT
>NEUR_homSap   DYVPEPFGTSCTLDWWLAQASVGGQVFILNILFFCLLLPTAVIVFSYVKIIAKVKS SSKEVAHFDSRIHSSHVLEMKLTKVAMLICAGFLIAWIPYAVVSVWSAFGRPDSIPIQLSVVPTLLAKSAAMYNPIIYQVIDYK FACCQTGGLK ATKKKSLEGFRLHTVTTVRKSSAVLEIHEEWE
>MEL_Platy     AYIPEGFQTSCTYDYLTQDMNNY--TYVLGMYLFGFIFPVAIIFFCYLGIVRAIFA HHAEMMATAKRMGAN...EIQIAKVAAMTIGTFMLSWTPYAVVGVFGMIKPHSEMFIH.AEIPVMMAKASARYNPIIYALSHPK FRAEIDKHFPWLLCCCKPKPKAQLPSSTTKGSIASKTEADTSV
>MEL1_homSap   AYVPEGLLTSCSWDYMSFTPAVR--AYTMLLCCFVFFLPLLIIIYCYIFIFRAIRE TGRALQTFGACKGNG.QSECKMAKIMLLVILLFVLSWAPYSAVALVAFAGYAHVLTPYMSSVPAVIAKASAIHNPIIYAITHPK YRVAIAQHLP CLGVLLGVSRRHSRPYPSYRSTHRSTLTSHTSNL

>PPINa_Ciona   YDTEGLGTSCAPNWFVKEKRERL--FIILYFVFCFVIPLAVIMICYGKLILTLRQ IAKESSLSGGTSPEGEVTKMVVVMVTAFVFCWLPYAAFAMYNVVNPEAQ IDYALGAAPAFFAKTATIYNPLIYIGLNRQ FRDCVVRMIF NGRNPWVDELVGSQVSSTGSQLTAVSSNKVAPA
>PPINb_Ciona   GYVPEGLGTSCAPNWFSKNKSER--IFIFVYFVFCFFIPLLVIIICYGKIVLFLKQVSLY ATRQSSASSNRQADNKVTKMVLVMISAFLICWTPYGVLSLYNAINPDKQ LDYGLGAVPVFFAKTANIYNPLIYIGLNKQ FRDGVIKMVF RGRNPWAEEMSTQQRQRSTEAGQPIVSNEV
>PPIN2_Ciona   SVIWHTPGLFFWNGYEPEGFGTS--CAPNWFSQQKRERIFIFAYFAFCFLTPLTIIFACYLKLILFIRKVSVSKKSMVNEADRRDFEVTRMVFVMIAAFLICWLPYGCLSMYNAIHPD FRDGVIRMLF KGRNPWLDGRNTTSSTSTRAQ

>scallop SCOP2 Patinopecten yessoensis scallop Mollusca
MPFPLNRTDTALVISPSEFRIIGIFISICCIIGVLGNLLIIIVFAKRRSVRRPINFFVLNLAVSDLIVALLGYPMTAASAFSNRWIFDNIGCKIYAFLCFNS
GVISIMTHAALSFCRYIIICQYGYRKKITQTTVLRTLFSIWSFAMFWTLSPLFGWS
SYVIEVVPVSCSVNWYGHGLGDVSYTISVIVAVYVFPLSIIVFSYGMILQEKVCKDSRKNGIRAQQRYTPRFIQDIEQRVTFISFLMMAAFMVAWTPYAIMSALAIGSFNVENSFAALPTLFAKASCAYNPFIYAFTNAN
FRDTVVEIMAPWTTRRVGVSTLPWPQVTYYPRRRTSAVNTTDIEFPDDNIFIVNSSVNGPTVKREKIVQRNPINVRLGIKIEPRDSRAATENTFTADFSVI

>scallop       
SYVIEVVPVSCSVNWYGHGLGDV--SYTISVIVAVYVFPLSIIVFSYGMILQEKVCSKNGIRAQQRYTPRFIQDIEQRVTFISFLMMAAFMVAWTPYAIMSALAIGSFNVENSFAALPTLFAKASCAYNPFIYAFTNAN



The key to timing rare genomic changes are opsin sequences from non-genomic lampreys which provide suitable probe to traces of Petromyzon maritimus, the lamprey chosen for a genome project. From traces, it can be verified that the 6 bp insert plus contemporary intron positions/phases (novel 12 upstream intron in LWS and 21 post-GWSR intron exclusively in rod/cone opsins) were already established by the time of lamprey divergence. Both rare genomic events occur between transmembrane helices TM2 and TM3, ie in extracellular loop 2. These two rare genomic changes -- in conjunction with  the absence of contradictory events and conventional clustering -- provide overwelming evidence against the oft-published tree sistering pinopsin with LWS to the exclusion of other cone opsins.

Despite 6 sequenced opsin mRNAs and an assembly in Branchiostoma, no rod/cone opsin can be located in it or earlier diverging deuterostomes (tunicate, amphioxus, urchin, acornworm, xenoturbella). These species may have larval eye spots and related photoreceptors but lack imaging eyes. Lamprey lack to date any opsin classifying within the PIN subtree but do contain modernly configured VAOP and PPIN, the latter in its pineal gland. Hagfish, sister group to lamprey, have imaging eyes but have not been studied; their opsins situation may be derived due to deepwater marine habitat (similarly deepwater coelocanth opsins are adapted to 420 nm). The next-diverging chondrichtyes have inadequate data -- only RHO1 from skate and fragments from Callirhyncus. 

In summary, full-blown pentachromatic color vision and rhodopsin appeared in the stem between amphioxus and lamprey divergence nodes. The oldest known fossil lamprey, Priscomyzon, dates at 360 myr to the Devonian has a full complement of modern opsins (other than parietal). Molecular clocks place lamprey divergence at approximately 430 myr, a hundred million years after Chengjiang.

The fossil record is unsatisfactory here: less than 1 bilateran in 10,000 in Chengjiang and Burgess Shale fossils is even a candidate for deuterostomy. Low numbers of specimens and poor preservation conspire with career ambitions to produce grandiose claims (published in Nature under controversial editor Henry Gi) that greatly exceed the data in the analysis of Hou, discoverer of the Chinese lagerstaette. Myllokunmingia is in the best situation with 500 specimens but Haikouichthys as stem deuterostome, Metaspreggina as post-ediacaran, and Yunnanozoan are all problematic. While signs of bilaterily disposed eyes are sometimes inferred, it does not follow these were image-forming eyes. Indeed contemporary Branchiostoma and tunicate larva have an eye-spot (ocellus); the genomes contain ciliary opsins clustering to approximately ENCEPH and PPIN -- still a long long road to imaging opsins. Echinoderms and hemichordates genomes have opsins but even more remote. Sea urchin genome encodes at least six opsins, four of these cluster classify to rhabdomeric, ciliary and Go-type. Tube feet are apparently the photosensory organ in adult urchins.

Meanwhile, thousands of high-quality Cambrian arthropod fossils unmistakably show stalked paired eyes. Imaging eyes of contemporary arthropods and lophotrochozoan are rhabdomeric, utilizing depolarizing Gq-type receptor, phospholipase C, phosphoinositola, diacylglycerol, and transient receptor potential TRP and TRPL channel signaling. However their genomes can also contain ciliary opsins, using hyperpolarizing Gt-type transducins and phosphodiesterase cGMP second-messaging (as well as Go-type gustducin ciliary opsins in other types of photoreceptors). Vertebrates are just the opposite, having crossed over to a ciliary opsin-based imaging system, while retaining rhabdomeric signaling in melanopsin retinal ganglion cells. Cnidarian opsins are available from Hydra and Nematostella genomes. Hydra expresses a ciliary-type opsin in ectodermal sensory nerve cells whereas Nematostella has opsins classifying between melanopsin and encephalopsin. It must not be thought that bilaterans invented imaging eyes because earlier diverging cubomedusan jellyfish Carybdea marsupialis has 4 eyestalks each with 6 photoreceptors of 4 types: simple eyespots, pigment cups, complex pigment cups with lenses, and camera-type eyes with a cornea, lens, and retina. This species needs a genome project.
 
Thus there is no evidence whatsoever -- and every reason to doubt from genomic analysis -- that deuterostomes had imaging eyes during the Cambrian. Despite this, a BBC series, Walking With Monsters, portrayed a school of 25 mm Haikouichthys attacking and wounding a 500 mm Anomalocaris. It is easy to guess at the scientific advisory panel. [This recurrent anthropocentric theme is echoed by fantastic museum imagery of early mammals nimbly predating on dinosaur nests -- dioramas quietly dismantled after Yucatan meteriorite discovery.] Imaging eyes are not essential to survival; even today subterranean mammals such as blind mole rat flourish without them. Discounting ray-finned fish numbers, a very substantial proportion of extant animal species lack imaging eyes 525 myr after the Cambrian. Of 33 animal phyla, a one-third have no specialized organ for detecting light, one-third have light-sensitive organs, and the remaining 6 have imaging eyes (Cnidaria, Mollusca, Annelida, Onychophora, Arthropoda, and Chordata). Thus 82% of animal phyla have survived well over 500 myr without imaging eyes despite competition/predation from animals with them. 

>RHO1_homSap rhodopsin                 <----------TM1--------->    c1     <----------TM2------->    x1      <c--i------TM3--------->           c2       <----------TM4-------->               x2         <----------TM5------c->     c3
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 
AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA* 0
           c3       <----------TM6------->    x3      <--------b-TM7---gprot>  helix8    palm cyto tail

 urochordate (1?), Cathaymyrus (cepahochordate, 1)

lungfish opsins> Neoceratodus can't find it ... have to query with rhodopsin as ncbi tool is too stupid.

did find doubly partial seq

>RHO1_Protopterus lungfish doubly partial seq
LAEPWKYSALAAYMFFLILVGFPINFMTLYVTIQHKKLRTPLNYILLNLAIGGLFMVFGGFTTTMYTSMNGYFVFGVTGCNIEGFFATFGGILGLWSLVV
LAIERYIVVCKPMSNFRFGENHAIMGIVFTWIMTLACAAPPLFGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFLIPLIIIFFCYGRLVCTV
KEAAAQQQESATTQKAEKEVTRMVYIMVISFLVCWLPYAFVAFYIFTHKGSDFGPVFMTAPAFFAKTAAFYNPVIYIFMNKQ 0
0 FRNCM      *0
  

The optics of the growing lungfish eye: Lens shape, focal ratio and pupillary movements in Neoceratodus forsteri (Krefft, 1870).
  Helena J Bailes , Ann E O Trezise , Shaun P Collin
Lungfish (order Dipnoi) evolved during the Devonian period and are believed to be the closest living relatives to the land vertebrates. Here we describe the previously unknown morphology of the lungfish eye in order to examine ocular adaptations present in early sarcopterygian fish. Unlike many teleosts, the Australian lungfish Neoceratodus forsteri possesses a mobile pupil with a slow pupillary response similar to amphibians. The structure of the eye changes from juvenile to adult, with both eye and lens becoming more elliptical in shape with growth. This change in structure results in a decrease in focal ratio (the distance from lens center to the retina divided by the lens radius) and increased retinal illumination in adult fish. Despite a degree of lenticular correction for spherical aberration, there is considerable variation across the lens. A re-calculation of spatial resolving power using measured focal ratios from cryosectioning reveals a low ability to discriminate fine detail. The dipnoan eye shares more features with amphibian eyes than with most teleost eyes, which may echo the visual needs of this living fossil.

AAD30519 coelocanth
>RHO1_Scyliorhinus canicula (catshark)
mngtegenfy ipmsnktgvv rspfdypqyy laepwkfsvl aaymffliia gfpvnfltly
       61 vtiqhkklrq plnyillnla vadlfmifgg fpstmitsmn gyfvfgpsgc nfegffatlg
      121 geiglwslvv laieryvvvc kpmsnfrfgs qhafmgvglt wimamacafp plvgwsryip
      181 egmqcscgid yytlkpevnn esfviymfvv hfsipltiif fcygrlvctv keaaaqqqes
      241 ettqraerev trmviimvia flicwlpyas vaffifcnqg sefgpifmti paffakaasl
      301 ynpliyilmn kqfrncmitt iccgknpfee eestsasask teassvsssq vapa

browser details OPNLW_ornAna    1087     1   364   364 100.0%  Ultra401  +-     228519    239398  10880
browser details OPNSW2_ornAna   1085     1   363   363 100.0%  Ultra401  +-     258788    263967   5180
>OPNLWS_ornAna green cone Ultra401:228519-239398
>OPNSWS2_ornAna blue cone Ultra401:258788-263967
Ultra401:239378-258808

platypus inline tandems intergenic gap 19,391 bp 10880 span 5180 span
<--LWS--<19k<--SWS2<
any internal intron markers? larger gen duP
how far back? chicken/liz? xenopus? teleost? 

probably very old association because 5 opsins in lamprey already. so if truly tandem, then has to be very old conserved-synteny dupl pre-lamprey
chicken genome missing but in mrna don't need
lizard both  scaffold_406:780,156-815,073
frog both scaffold_275:171,667-235,246 but showing signs of 3rd lws frag pseudo
zfish oddly has 4=3+1 in a row!  chr11:26,179,088-26,677,303 but still all about sws2 and lws1
unfortunately no chance of callo contig
lamprey be a mess
branchio lacks all cones

>OPNLW_ornAna green cone -Ultra401:228519-23939 minus strand
MTPAWNSGVYAARRRFEDEEDTTRTSVFVYTNSNNTRDPFEGPNYHIAPRWAYNVTSLWM
IFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFI
LGHPMCVLEGYTVSLCGITGLWSLSIISWERWIVVCKPFGNVKFDAKLAMVGIVFSWVWA
AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIVLCYL
QVWLAIRAVAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTIFACFAAANPGYAFH
PLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKVDDGSELSSTSRTEVSSVSSVSPA*

>OPNSW2_ornAna blue cone -Ultra401:258788-263967 minus strand
MHKTHRNLQNELPEDFFIPLPLDTDNITSLSPFLVPQTHLGGSGIFMSLAAFMFLLITLG
FPINLLTVICTIKYKKLRSHLNYILVNLAVSNMLVVCVGSATAFYSFAHMYFVLGPTACK
IEGFAATLGGMVSLWSLAVIAFERFLVICKPLGNLSFRGTHAIFGCAATWVFGLAASLPP
LFGWSRYIPEGLQCSCGPDWYTTNNKWNNESYVIFLFSFCFGVPLSIIIFSYGRLLLTLR
AVAKQQEQSATTQKAEREVTKMVIVMVLGFLVCWLPYASFSLWVVTNRGQVFDLRMASIP
SVFSKASTIYNPIIYVFMNKQFRSCMLKLVFCGKSPFGDEDEISGSSQATQVSSVSSSQVSPA*


Here's a memo i wrote on 4 color vision in platypus ancestor:

	From: 	  tom@cyber-dyne.com
	Subject: 	proof that ancestral mammal had trichromatic vision
	Date: 	September 7, 2007 11:41:38 AM PDT
	To: 	  platypus@watson.wustl.edu

wes,

I really like the new title. The broader constituency probably prefers ancestral mammal genome content to platypus-specific biology; the platypus divergence date nicely breaks up the long branch to chicken and anole. I worked out a longwinded example below illustrating how the platypus genome can successfully bridge a long-standing gap in our understanding of mammalian color vision evolution.

I had to carefully distinguish genomic reconstructions of last common ancestors (beyond our remit) from initial inferences based on early assemblies of extant species. Absence of assembly evidence does not constitute evidence of genomic absence but more commonly lack of coverage, even when unused raw traces among the 33,353,710 total are consulted.

Protein-coding genes in the platypus have been evolving fairly rapidly under selection over the same 166 million years as eutherians -- the tree of life is right-justified. While 'living fossils' do exist (species with slowly evolving proteomes), the platypus is not one of them. On the contrary, picking a protein at random from pre-bilateran Nematostella and employing blastp against all mammals, the human ortholog is most commonly top hit (ie least evolved). Platypus proteins rarely surface as best-blast.

Comparative genomics does not support the conceit of evolutionary progress chugging steadily along to a pinnacle of human innovation even as primitive creatures drop by the wayside for want of manifest destiny. We know today the platypus genome does not encode any ancient, ancestral, antiquated, archaic, dead-end, failed-experiment, fossil, frozen, primitive, primordial, relic, retro or stationary genes. Indeed platypus genes in conserved syntentic position to bird and lizard homologs but lost in human represent genome content (and often functionality) conserved in ancestral mammal but gone in placentals.

As well-known example, contemporary amniote eyes have demonstrably superior color vision (four cone opsins and improved spectral resolution from pigmented oil droplets) relative to those of nocturnally degenerated placental mammal, as proposed by Gordon Walls in 1942 (ref 1). 

Opsins don't lend themselves to simple homology-based parsimony reconstructions because of evolutionary convergence of experimentally accessible (spectroscopic) properties and lineage-specific expansions and contractions. What's needed here are complete genomes and syntenic validation of orthology, which we lack to a certain degree here in key species (eg 3 of 6 known chicken opsins are missing from its current assembly).

However using the platypus genome, I've now been able to reliably reconstruct the cone opsin situation in ancestral mammal, building on ref 2. This is a difficult argument because platypus assembly initially exhibits only exon 5 of an opsin gene clustering to the short wavelength sensitive opsin SWS1 (as observed in ref 2). 

Close synteny analysis of the gapless platypus assembly contig 45.4 using a conserved non-coding phastCons marker and adjacent CALU gene shows that exons 1-4 do not lie in adjacent assembly gaps but were lost in a multi-kbp deletion. Exon 5 exhibits a small number of disabling non-synonymous changes despite retaining overall high (63%) sequence identity to human, consistent with millions of years of normal divergence followed by rapid neutral evolution after the deletion of exons 1-4 pseudogenized residual exon 5. The deletion can be heuristically dated to perhaps 40 mya, an estimate that echidna SWS1 sequence would greatly improve. No opsin data currently exists for echidna; they may retain functional SWS1.

It follows that ancestral monotreme resp. ancestral mammal had 3-color vision (one step down from ancestral amniote) even though the platypus itself today has 2-color vision (similar to marsupials and most placentals). (This assumes intact SWS1 was not exapted to some unrelated function; this is testable from its spectral reconstruction.)

contempory:
 chicken   (SWS1  SWS2  LWS RHO2 RHO1) 4-color cone vision + 1 rod opsin
 platypus  (SWS1- SWS2  LWS ---  RHO1) 2-color cone vision + 1 rod opsin
 marsupial (SWS1  ---   LWS ---  RHO1) 2-color cone vision + 1 rod opsin  
 elephant  (SWS1  ---   LWS ---  RHO1) 2-color cone vision + 1 rod opsin
 human     (SWS1    LWSa/LWSb    RHO1) 3-color cone vision + 1 rod opsin

ancestral:
 amniote   (SWS1  SWS2  LWS RHO2 RHO1) 4-color cone vision + 1 rod opsin
 mammal    (SWS1  SWS2  LWS ---  RHO1) 3-color cone vision + 1 rod opsin
 theran    (SWS1  ---   LWS ---  RHO1) 2-color cone vision + 1 rod opsin  
 placental (SWS1  ---   LWS ---  RHO1) 2-color cone vision + 1 rod opsin
 hominids  (SWS1    LWSa/LWSb    RHO1) 3-color cone vision + 1 rod opsin


Details:

Queries by known SWS1 genes -- but not other opsins -- return a strong match to platypus chr10:3,960,795-3,960,908, which translates to FHACIMEMMRGKLMVDDSESSSQETKTSTVSSRQVGPS* with conserved intron position and phase zero characteristic of SWS1 exon 5. The 11,205 bp contig 45.4 also contains terminal exons of long-conserved syntenic gene CALU in the expected opposite strand orientation. Total coding gene span seems short enough (3,646 bp in opossum, 3,248 bp in human, 11,959 bp in anole) that the contig might be expected to contain some or all of exons 1-4 as well, even adjusting contig length to reflect observed lineage-specific retroposons of platypus. However exons 1-4 are missing from the contig and indeed the assembly. Furthermore missing exons cannot be found among GenBank transcripts now raw trace reads which include singleton reads and reads from other centers not used in the assembly.

This raises the question whether platypus lacks full length SWS1 or whether exons 1-4 merely lie in nearby gaps of the current 6x assembly. Possibly earlier introns have expanded so much that exons 1-4 have been pushed off the contig into these gaps. However contig 45.4 contains the phylogenetically conserved non-coding phastCons element lod109 (ref 3) at its extreme 3' end chr10:3,964,439-3,964,588 (the contig ends at 3,964,658!).

The UCSC genome browser provides putative orthologs of lod109 in marsupial and placental. These blat as standalone queries into full syntenic position with matching strand orientation with respect to marsupial and mouse where they are named lod15+lod45 and lod78 respectively. Here phastCons strand convention, which is inherently arbitrary, can be taken as positive for platypus and carried forward to mouse and oppossum. CALU is positive but SWS1 exon 5 is negative in all three species. 

Thus exons 1-4 of platypus are required to lie between SWS1 exon 5 and lod109, a region spanned by a single gapless contig, but they do not. This requires either a deletion or translocation elsewhere (to a trace read and assembly gap). A local inversion might move exons 1-4 into an assembly gap but that would disrupt reading frame. Implausibly, the missing exons could be translocated into an adjacent bridged gap of estimated modest size preceding the right-flanking gene NAG6 while retenting strand; this is incompatible with all four exons remaining recalcitrant to repeated attempts at genomic amplification (ref 2) and still missing in 6x coverage. 

In summary, SWS1 is non-functional in platypus because the highly conserved exons 1-4 critical to opsin structure and function have been deleted. Conceivably this could be a copy-number polymorphism specific to the individual female platypus chosen for the genome project -- a seemingly viable concern given such polymorphisms are common for the tandem chrX opsin array in human. [Note the current human assembly shows 3 tandem opsins on chrX!] However platypus SWS1 does not lie in tandem array that might foster frequent inhomogeneous recombination. Human colorblindness involving loss of orthologous SWS1 is quite rare. 

Further close analysis of exon 5 shows the deletion event lies between ancient and recent:

Alignment of orthologous exons from 19 species phylogenetically bracketing platypus establish an arginine anomalously replacing conserved cysteine and a one residue deletion in platypus but otherwise very respectable percent identity that is not compatible with gene loss 166 mya ago (date for divergence taken in platypus paper). Non-selected pseudogenized coding dna does not leave detectable remnants at this age -- indeed no remnants can be detected of amniote RHO2 in mammals nor SWS2 in therans even focusing the search on syntenic dna, ref 2 and here. 

>OPNSWS1_xenTro FRGCIMETVCGRPMTDDSSVSSTSQKTEVSTVSSSQVSPA* amphibian
>OPNSWS1_anoCar FRACILETVCGKPMSDESDVSSSAQKTEVSSVSSSQVSPS* lizard
>OPNSWS1_pheMad FRGCIMEMVCGKPMSDDSEASTS-QKTEVSSVSSSQVSPS* lizard
>OPNSWS1_gekGek FRGCILEMVCGKTMAEESEVSSASQKTEVSSVSSSQVGPS* lizard
>OPNSWS1_utaSta FRACIMETVCGKPMTDESDVSSSAQKTEVSSVSSSQVSPS* lizard
>OPNSWS1_galGal FRACIMETVCGKPLTDDSDASTSAQRTEVSSVSSSQVGPT* bird
>OPNSWS1_taeGut FRACIMETVCGRPMTDDSEVSSSAQRTEVSSVSSSQVGPS* bird
>OPNSWS1_phaCar FRACIMETVCGKPMADDSEASSSAQRTEVSSVSSSQVSPS* bird
>OPNSWS1_ancMam FHACIMEMVCGKPMTDDSdVSSS-QKTEVSTVSSSQVGPS* ancestral mammal
>OPNSWS1_ornAna FHACIMEMMRGKLMVDDSE-SSS-QETKTSTVSSRQVGPS* monotreme
>OPNSWS1_monDom FHACIMEMVCRKPMTDDSDVSSS-QKTEVSAVSSSQVGPT* marsupial opossum Didelphimorphia
>OPNSWS1_macEug FHACIMEMVCRKPMTDDSEASSS-QKTEVSTVSSSQVGPS* marsupial wallaby Diprotodontia
>OPNSWS1_smiCra FHACIMEMICKKPMTDDSETTSS-QKTEVSTVSSSQVGPS* marsupial dunnart Dasyuromorphia
>OPNSWS1_setBra FHACIMEMVCRKPMTDDSEASSS-QKTEVSTVSSSQVGPS* marsupial quokka Diprotodontia
>OPNSWS1_isoObe FHACIMEMICRKPMTDDSETSSS-QKTEVSTVSSSQVSPS* marsupial bandicoots Peramelemorphia
>OPNSWS1_canFam FRACIMEMVCGKSMTEDSEMSSS-QKTEVSTVSPSQVGPN* placental
>OPNSWS1_susScr FRACIMEMVCGKPMTDESDMSSS-QKTEVSTVSSTQVGPN* placental
>OPNSWS1_homSap FQACIMKMVCGKAMTDESDTCSS-QKTEVSTVSSTQVGPN* placental
>OPNSWS1_sciBol FRACIMEMVCGKAMTDESDISSS-QKTEVSTVSSSQVGPN* placental
>OPNSWS1_cavPor FRACIMELVCRKPMADESDMSTS-QKTEVSAVSSSKVGPN* placental
>OPNSWS1_musMus FRACILEMVCRKPMADESDVSGS-QKTEVSTVSSSKVGPH* placental
     Consensus  FraCImEmvcgkpMtD#S#.sss.QkTevStVSSsqVgP.*

The anomalous arginine can be validated in raw trace data, necessary because the trace assembly process resolves discrepancies by quality scores weighting that might disadvantage a read more accurate locally at the cysteine position. Viewing original data requires blastn against sepaate platypus WGS and OTHER databases at the NCBI trace archive repository. Some 752,000 additional traces from TIGR and NISC are found there in addition to 3,595,283 cDNA WUGSC traces. These numbers are a significant addition to the 27,607,516 conventional WGS traces used (but not used up) in the current platypus assembly.

The usual error types occur in these traces but none would result in R --> C and similarly for the 3bp indel. This cysteine is deeply conserved in homologous position in other opsins such as RHO1, SWS2, and LWS though there is 6 residues of spacing in the latter two families instead of 5 here.Therefore arginine, manifestly unsuited for a disulfide bond, is not acceptable structurally in this position.  

The amino acid in platypus is a bit unusual at four other sites, highlighted in red in the alignment. Some of these changes may be incapacitating but others tolerated or even advantageous.  While other species have their anomalies as well, platypus is a real outlier in this regard which can be seen for example by MultiAlign tree construction. http://bioinfo.genopole-toulouse.prd.fr/multalin/multalin.html  

The alignment contains a heuristic prediction of exon 5 in the last common ancestor of mammals that is useful in counting changes in descendant lineages. Overall platypus exon 5 has evolved anomalously in that its variations are not concentrated at commonly variable positions but disproportionately at conserved ones, a pattern characteristic of a pseudogene. Opsin change is difficult to assess because to be retained over long timeframes, SWS1 and SWS2 in the same species may push each other apart (subfunctionalize) at significant sites that affect absorption spectra (eg color vision) rather than just drift at soft positions. 

Platypus exon 5 can only have become nonfunctional fairly recently -- retaining 63% identity to human given 332 mya of round-trip evolutionary time is quite respectable and implies long periods of conserved functionality. (Chicken/human have 65% identity.) This degree of conservation is incompatible with ancestral monotreme already having pseudogenized SWS1 from consideration of neutral rates. Thus it appears that a platypus ancestor, possibly prior to echidna divergence at 25 mya (ref 4), still had functional SWS1 and so trichromatic cone vision. That would also be true further back at the ancestral mammalian node because platypus retains SWS2 and LWS, still in amniote-syntenic tandem position at Ultra401:228519-263967 (blat genome or see ref 2).

In summary, the preferred scenario is platypus ancestors possessing a functional SWS1 gene evolving at a moderate rate until the fairly recent deletion of exons 1-4. After the deletion the remaining exon 5 had no constraints and so evolved at the faster neutral rate of pseudogenic dna.

How recent was this deletion? That would require partitioning changes in platypus exon 5 since divergence from ancestral mammal between drift and selective change during the functional era from subsequent neutral change in the pseudogene era, based on anomalous character and what is known generally about opsin evolution and neutral rates in general. That calculation would greatly benefit from determining the sequence and status of exon 5 in echidna. If echidna still had functional SWS1 and the divergence time was 25 mya, the deletion event in platypus must post-date that. On the other hand, if echidna also contained the indel, the departure of its exon 5 sequence from platypus would significantly inform event partitioning and so improve dating of the indel.

It cannot be proven that intact SWS1 functioned as a cone cell color vision receptor in ancestral platypus (because opsins can be exapted to other purposes); echidna sequence might at least allow appropriateness of its adsorption spectrum to be adduced.

ref 1
Walls, GL
The Vertebrate Eye and its Adaptive Radiation
Cran brook Institute 1942
TOC http://www.crsltd.com/research-topics/walls/index.html

ref 2
Davies WL, Carvalho LS, Cowing JA, Beazley LD, Hunt DM, Arrese CA
Visual pigments of the platypus: a novel route to mammalian colour vision.
Curr Biol. 2007 Mar 6;17(5):R161-3. 

ref 3
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. 
Genome Res. 2005 Aug;15(8):1034-50.
 
ref 4
Pettigrew JD.	
Electroreception in monotremes.
J Exp Biol. 1999 May;202(Pt 10):1447-54.
http://jeb.biologists.org/cgi/reprint/202/10/1447

>lod109_ornAna+ chr10:3964439-3964588 
tgctgctgatgtggcaaagaagaccacatctgtccagctacttctatcaccggctcgttggtctaggggtatgattctcgcttagggtgcgagaggtcccgggttcaaatcccggacgagccctgtttttcccacctggttttatttggg

>lod109_monDom+  chr8:184,539,020-184,560,157 from platypus alignment
tgctgatgatgtggcaaaaccacatctggacaactattttcaacactggctcgttggtctaggggtatgattctcgcttagggtgcgagaggtcccgggttcaaatcccggacgagcccaattttac

>lod78_musMus+ chr6:29338830-29338906 from platypus alignment
tgttgatgatgtggtagag-aggatacatctggccaggagtaaccgccagtggctcgttggtctaggggtatgattctcgcttagggtgcgagaggtcccgggttcaaatcccggacgagccctgcttatc

genomic data availability relative to chicken
LWS  galGal- ornAna+ homSap++
SWS2 galGal- ornAna+ homSap+  
SWS1 galGal- ornAna- homSap+
RHO2 galGal+ ornAna- homSap- 
RHO1 galGal+ ornAna+ homSap+
PPNG galGal+ ornAna- homSap-

>OPNLW_ornAna green cone Ultra401:228519-23939
MTPAWNSGVYAARRRFEDEEDTTRTSVFVYTNSNNTRDPFEGPNYHIAPRWAYNVTSLWM
IFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFI
LGHPMCVLEGYTVSLCGITGLWSLSIISWERWIVVCKPFGNVKFDAKLAMVGIVFSWVWA
AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIVLCYL
QVWLAIRAVAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTIFACFAAANPGYAFH
PLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKVDDGSELSSTSRTEVSSVSSVSPA*

>OPNSW2_ornAna blue cone pigment Ultra401:258788-263967
MHKTHRNLQNELPEDFFIPLPLDTDNITSLSPFLVPQTHLGGSGIFMSLAAFMFLLITLG
FPINLLTVICTIKYKKLRSHLNYILVNLAVSNMLVVCVGSATAFYSFAHMYFVLGPTACK
IEGFAATLGGMVSLWSLAVIAFERFLVICKPLGNLSFRGTHAIFGCAATWVFGLAASLPP
LFGWSRYIPEGLQCSCGPDWYTTNNKWNNESYVIFLFSFCFGVPLSIIIFSYGRLLLTLR
AVAKQQEQSATTQKAEREVTKMVIVMVLGFLVCWLPYASFSLWVVTNRGQVFDLRMASIP
SVFSKASTIYNPIIYVFMNKQFRSCMLKLVFCGKSPFGDEDEISGSSQATQVSSVSSSQVSPA*

>OPNRH_ornAna rhodopsin rod pigment Ultra20:114,479-118,391
MNGTEGQDFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSVLAAYMFMLIMLGFPINFLTLY
VTIQHKKLRTPLNYILLNLAFANHFMVLGGFTTTLYTSLHGYFVFGPTGCNIEGFFATLG
GEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACALPPLVGWSRYIP
EGMQCSCGIDYYTLRPEVNNESFVIYMFVVHFTIPMTIIFFCYGRLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTVPAFFAKSSAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATASKTEQSSVSTSQVSPA*

>OPNSWS1_ornAna terminal exon chr10:3,935,884-3,985,883 
FHACIMEMMRGKLMVDDSESSSQETKTSTVSSRQVGPS*