Marsupial phyloSNPs

Introduction to Marsupial phyloSNPs

In this project, new genomic data from the Tasmanian devil (Sarcophilus harrisii), Tasmanian tiger (Thylacinus cynocephalus), and echidna (Tachyglossus aculeatus) are analyzed for significant changes at the protein coding level. The goal is to find single amino acid changes in one of these species at a highly invariant residue in a well-conserved exon in a gene with known or predictable tertiary structure. Such changes are thought to enrich for genetic changes with significant, adaptive biochemical or phenotypic consequences (1,2,3,4), in contrast to ordinary SNPs at positions of low conservation. Thus phyloSNPs are informative to the distinctive biology of the species carrying them and suggest a focus for subsequent experiment.

It is also of particular interest to determine the levels of variation within the Tasmanian devil population as a whole because the number of individuals have become low and possibly inbreed with adverse sequelae. For this it will be necessary to first determine sites of variation and then to genotype them across a large number of individuals.

Marsupial genomic and cDNA data to date has been quite limited compared to placental mammal. Yet as outgroup, metatheran animals provide important context to placentals and represent important context in understanding human protein evolution. The monotheres are inevitably limited by the paucity of extant species (basically platypus and echidna) and dim prospects for fossil DNA. Consequently echidna provides an important adjunct to the existing but incomplete platypus assembly. While extant birds and reptiles -- the preceding divergence node -- are abundant it must be remembered that a very considerable time elapsed (from 310 mry to 175 mry) prior to divergence of mammals with living representatives. This gap of 135 myr is comparable to the whole evolutionary record of theran mammals.

Assumed vertebrate phylogenetic tree

Marsupial relationships taken from 2009 paper establishing the mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus):

Newick tree that generates vertebrate phylogenetic tree used in the analysis here:

((((((((((((((((((homSap,panTro),gorGor),ponPyg),macMul),calJac),tarSyr),(micMur,otoGar)),tupBel),
(((((musMus,ratNor),dipOrd),cavPor),speTri),(oryCun,ochPri))),
(((((vicPac,susScr),turTru),bosTau),((equCab,(felCat,canFam)),(myoLuc,pteVam))),(eriEur,sorAra))),
(((loxAfr,proCap),echTel),(dasNov,choHof))),
(monDom,((macEug,triVul),(sarHar,thyCyn)))),
(ornAna,tacAcu)),
((galGal,taeGut),anoCar)),
xenTro),
(((tetNig,takRub),(gasAcu,oryLap)),danRer)),
calMil),
petMar);

Phylo-sorting data

This tab-delimited table enables four different sort orders. These are needed because data can be missing from species in a manner that varies by gene, making data alignment difficult. Some alignment tools also lose input order, so that needs to be recovered. The ordering here flattens the phylogenetic tree by taking human (arbitrarily) at the top and resolving ambiguous situations (eg mouse, rat) by putting species with the best assemblies first.

The first two columns provide sort order number for the 44 species alignment at UCSC as phylogenetic and alphabetic order respectively. The third and fifth columns do this for a larger set of species for which data is commonly available. The fourth column provides a fasta line indicator. The sixth column is a dummy gene name to be replaced as needed. The next column has stripped out the syntax from Newick tree format. This column and column six together will correctly draw the vertebrate phylogenetic tree in all online software without further editing. The final columns provide genus, species, and common name.

-	-	-	-	-	-	-	((((((((((((((((((	-	-	-	-
10	26	10	>	27	gene	homSap	,	Homo	sapiens	(human)	hg181
11	38	11	>	40	gene	panTro	),	Pan	troglodytes	(chimp)	panTro
12	25	12	>	26	gene	gorGor	),	Gorilla	gorilla	(gorilla)	gorGor
13	40	13	>	42	gene	ponPyg	),	Pongo	pygmaeus	(orang)	ponAbe
14	28	14	>	30	gene	macMul	),	Macaca	mulatta	(rhesus)	rheMac
15	12	15	>	12	gene	calJac	),	Callithrix	jacchus	(marmoset)	calJac
16	48	16	>	53	gene	tarSyr	),(	Tarsius	syrichta	(tarsier)	tarSyr
17	29	17	>	31	gene	micMur	,	Microcebus	murinus	(mouse_lemur)	micMur
18	37	18	>	39	gene	otoGar	)),	Otolemur	garnettii	(bushbaby)	otoGar
19	50	19	>	57	gene	tupBel	),(((((	Tupaia	belangeri	(tree_shrew)	tupBel
20	31	20	>	33	gene	musMus	,	Mus	musculus	(mouse)	mm91
21	43	21	>	45	gene	ratNor	),	Rattus	norvegicus	(rat)	rn41
22	18	22	>	19	gene	dipOrd	),	Dipodomys	ordii	(kangaroo_rat)	dipOrd
23	14	23	>	15	gene	cavPor	),	Cavia	porcellus	(guinea_pig)	cavPor
24	45	24	>	48	gene	speTri	),(	Spermophilus	tridecemlineatus	(squirrel)	speTri
25	35	25	>	37	gene	oryCun	,	Oryctolagus	cuniculus	(rabbit)	oryCun
26	33	26	>	35	gene	ochPri	))),(((((	Ochotona	princeps	(pika)	ochPri
27	52	27	>	59	gene	vicPac	,	Vicugna	pacos	(lama)	vicPac
54	57	28	>	49	gene	susScr	),	Sus	scrofa	(pig)	
28	51	29	>	58	gene	turTru	),	Tursiops	truncatus	(dolphin)	turTru
29	11	30	>	11	gene	bosTau	),((	Bos	taurus	(cow)	bosTau
30	20	31	>	21	gene	equCab	,(	Equus	caballus	(horse)	equCab
31	22	32	>	23	gene	felCat	,	Felis	catus	(cat)	felCat
32	13	33	>	14	gene	canFam	)),(	Canis	familiaris	(dog)	canFam
33	32	34	>	34	gene	myoLuc	,	Myotis	lucifugus	(microbat)	myoLuc
34	42	35	>	44	gene	pteVam	))),(	Pteropus	vampyrus	(macrobat)	pteVam
35	21	36	>	22	gene	eriEur	,	Erinaceus	europaeus	(hedgehog)	eriEur
36	44	37	>	47	gene	sorAra	))),(((	Sorex	araneus	(shrew)	sorAra
37	27	38	>	28	gene	loxAfr	,	Loxodonta	africana	(elephant)	loxAfr
38	41	39	>	43	gene	proCap	),	Procavia	capensis	(hyrax)	proCap
39	19	40	>	20	gene	echTel	),(	Echinops	telfairi	(tenrec)	echTel
40	17	41	>	18	gene	dasNov	,	Dasypus	novemcinctus	(armadillo)	dasNov
41	15	42	>	16	gene	choHof	))),(	Choloepus	hoffmanni	(sloth)	choHof
42	30	43	>	32	gene	monDom	,((	Monodelphis	domestica	(opossum)	monDom
55	55	44	>	29	gene	macEug	,	Macropus	eugenii	(wallaby)	
56	56	45	>	46	gene	sarHar	),(	Sarcophilus	harrisii	(tasmanian_devil)	
57	60	46	>	56	gene	triVul	,	Trichosurus	vulpecula	(bushytail_possum)	
58	59	47	>	55	gene	thyCyn	)))),(	Thylacinus	cynocephalus	(tasmanian_tiger)	
43	34	48	>	36	gene	ornAna	,	Ornithorhynchus	anatinus	(platypus)	ornAna
59	58	49	>	50	gene	tacAcu	)),((	Tachyglossus	aculeatus	(echidna)	
44	23	50	>	24	gene	galGal	,	Gallus	gallus	(chicken)	galGal
45	46	51	>	51	gene	taeGut	),	Taeniopygia	guttata	(finch)	taeGut
46	10	52	>	10	gene	anoCar	)),	Anolis	carolinensis	(lizard)	anoCar
47	53	53	>	60	gene	xenTro	),(((	Xenopus	tropicalis	(frog)	xenTro
48	49	54	>	54	gene	tetNig	,	Tetraodon	nigroviridis	(pufferfish)	tetNig
49	47	55	>	52	gene	takRub	),(	Takifugu	rubripes	(fugu)	fr21
50	24	56	>	25	gene	gasAcu	,	Gasterosteus	aculeatus	(stickleback)	gasAcu
51	36	57	>	38	gene	oryLap	)),	Oryzias	latipes	(medaka)	oryLat
52	16	58	>	17	gene	danRer	)),	Danio	rerio	(zebrafish)	danRer
60	54	59	>	13	gene	calMil	),	Callorhinchus	milii	(elephantfish)	
53	39	60	>	41	gene	petMar	)	Petromyzon	marinus	(lamprey)	petMar
											
44	44	51	f	51	gene	fasta	tree_syntax	genus	species	common	ucsc
phy	alp	phy		alp

Candidate analysis

The first issue is error within the reads themselves; the second is whether the default 454 Newbler assembler correctly identified overelapping reads and put them together properly to give exon-spanning reads. Those issues are discussed elsewhere -- here it is assumed the data is correct, so the entire focus is on subsequent bioinformatics.

(methods explained more shortly)

Case of ERN2

chr6_5971 ERN2 4
contig00001  length=355   numreads=5
KLPFTIPELVHASPCRSSDGVLYT
.....................F..
               ^        
15      R=3(75) H=2(50

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by L->F), then differences between the two thylacines
(here one individual has R at position 15, the other has H), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues: ERN2 has not generated potentially confusing recent processed pseudogenes in mammals (lack of human, opossum or platypus genome Blat matches to ERN2 query). The variation observed here between individual tasmanian devils is implausibly an early stage in the loss of parent gene because of ERN2 functional essentiality; the exon cannot come from a decaying segmental duplication because coverage is high enough to also detect the main gene.

Paralog issues: The GeneSorter tool at UCSC shows a single significant full-length paralog in human, ERN1, also with 22 coding exons. The genes reside on different chromosomes but in regions with local homology of synteny. However this particular exon is a good match (3 differences out of 23), so there is potential for experimental difficulties in distinguishing them in short reads (including the following exon readily resolves them bioinformatically). In any event, at positions 15 and 20, ERN1 is identical at the amino acid level to ERN2. The gene duplication appears to have occured subsequent to amphioxus divergence earlier diverging metazoans are single-copy.

Homoplasy (recurrent mutation) issues: This exon is very conserved and does not exhibit repetitive sequence, compositional simplicity, or indels in any species in either paralog that could foster experimental error or alignment ambiguity. At position 15, the ancestral value is arginine in both paralogs. The G--> A transition to histidine in one individual is conservative under most circumstances (still basic) and arises from an arginine codon CpG hotspot conserved back to lamprey in 30 of 32 species with available data, yet histidine is not observed part of a reduced alphabet (ie R/H) at this position over many billions of years of branch length. Consequently R-->H is a significant change in this individual tasmanian devil.

Known variations: No human disease variants have been reported for either ERN2 or ERN1, probably attributable to essentiality. Site-specific mutation close to the exon here have been generated for K121P, D123P, W125A, and Q105E but only for ERN1. Naturally occuring coding SNPs in the human population relevent to the ERN2 exon are not known but low frequency alleles could emerge from the 1000 Genomes Project.

Side issues: a very ancient conserved leucine at position 21 appears to be transitioning to phenylalanine at marsupial node but has not been fixed, so settles out as L or F depending on lineage-sorting on each terminal marsupial leaf whereas placentals are all changed to phenylalanine (a phyloSNP caught in mid-air). While L and F might seem about the 'same' as amino acids, the branch length conservation totals say both are important but for different reasons: this is not a waffle codon nor reduced alphabet situation. This raises the question -- given the extreme conservation of this exon otherwise -- of whether the L-->F change at position 21 in both individuals has 'enabled' (made neutral or adaptive) an otherwise unfavorable R-->H change at position 15 in one individual.

Structural significance: By good fortune, the crystal structure of ERN1 (alternately called IRE1) has been published. The PDB 2HZ6 structure has good coverage of this particular exon. Consequently the marsupial ERN2 could be very accurately modelled and the structural effects of L-->F with or without R-->H computed by submission to online SwissProt modelling service.

Monodelphis ERN2 (key exon: sarHar2) aligned to human ERN1 luminal domain 
 Expect = 5.8e-65 Identities = 109/180 (60%), Positives = 141/180 (78%)

ERN2_monDom   1  PESLLFISTLDGSLHAVSKKTGDIQWTLKDDPIIQGPVYATEPAFLPDPSDGSLYILGEE  60
                 PE+LLF+STLDGSLHAVSK+TG I+WTLK+DP++Q P +  EPAFLPDP+DGSLY LG +
ERN1_homSap   8  PETLLFVSTLDGSLHAVSKRTGSIKWTLKEDPVLQVPTHVEEPAFLPDPNDGSLYTLGSK  67

ERN2_monDom  61  SKQGLMKLPFTIPELVHASPCHSSDGVFYTGRKQDTWFMVDPKSGKKQTMLSTETWDGLY  120
                 + +GL KLPFTIPELV ASPCRSSDG+LY G+KQD W+++D  +G+KQ  LS+   D L 
ERN1_homSap  68  NNEGLTKLPFTIPELVQASPCRSSDGILYMGKKQDIWYVIDLLTGEKQQTLSSAFADSLC  127

ERN2_monDom  121 PSAPLLYIGRTQYTVTMYDPRSQALRWNTTYRGYSAPLLDHLPGYQVGHFTCSGEGLVVT  180
                 PS  LLY+GRT+YT+TMYD +++ LRWN TY  Y+A L +    Y++ HF  +G+GLVVT
ERN1_homSap  128 PSTSLLYLGRTEYTITMYDTKTRELRWNATYFDYAASLPEDDVDYKMSHFVSNGDGLVVT  187

Functional significance: A considerable amount is known about the paralog ERN1. Annotation transfer is likely applicable to ERN2. The two gene products differ primarily in expression -- ERN1 ubiquitious but ERN2 restricted to intestinal epithelial cells:

"The unfolded protein response (UPR) is an evolutionarily conserved mechanism by which all eukaryotic cells adapt to the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring kinase 1 (IRE1 or ERN1) and PKR-related ER kinase (PERK) are two type I transmembrane ER-localized protein kinase receptors that signal the UPR through a process that involves homodimerization and autophosphorylation... The monomer of the luminal domain comprises a unique fold of a triangular assembly of beta-sheet clusters. Structural analysis identified an extensive dimerization interface stabilized by hydrogen bonds and hydrophobic interactions... Mutations that disrupt the dimerization interface produced ERN1 protein that failed to either dimerize or activate the UPR upon ER stress."

"ERN1 is a type I transmembrane protein kinase receptor that also has a site-specific RNase activity that, upon activation, initiates a site-specific unconventional splicing reaction. The substrate for IRE1 RNase in metazoans is Xbp1 mRNA, which encodes a basic leucine zipper transcription factor of the ATF/CREB family. XBP1 controls expression of genes containing an X-box element or a UPR element in their promoter regions. The IRE1-mediated splicing reaction introduces into XBP1 an alternative C terminus, thereby generating an XBP1 molecule that is a more potent transcriptional activator. Therefore, activation of IRE1 and its RNase increases the transcription of genes encoding ER chaperones and folding catalysts... the ERN1 N-terminal luminal domain (NLD) functions as an ER stress sensor... under normal conditions IRE1 is maintained in a monomeric state through interaction of the NLD with the ER resident chaperone BiP. Upon ER stress, Grp78 binds to unfolded proteins as they accumulate, permitting the released NLD to form homodimers. Dimerization of the NLD in turn leads to the activation of the protein kinase and RNase activities in the cytosolic domain of ERN1."

ENR2 is readily distinguished from its ERN1 paralog at tBlastn by including the two following exons which bring percent identity to 62%:

ERN2_monDom KLPFTIPELVHASPCRSSDGVLYTGRKQDTWFMVDPKSGKKQTMLSTETWDGLYPSAPLLYIGRTQYTVTMYDPRSQALRWNTTYRGYSA
            KLPFTIPELV ASPCRSSDG+LY G+KQD W++VD  +G+KQ  LS+   + L PS  LLY+GRT+YT+TM+D +S+ LRWN TY  Y+A
ERN1_monDom KLPFTIPELVQASPCRSSDGILYMGKKQDIWYVVDLMTGEKQQTLSSAFAESLCPSTSLLYLGRTEYTITMFDTKSRELRWNATYFDYAA

The first alignment shows ERN2 orthologs in vertebrates, the second as difference relative to opossum, the third ERN1 orthologs.
The ancestral nature of the CpG hotspot is shown in nucleotides in the final columns.

                            ^     *                                ^     *                                 ^     *  
ERN2_homSap  KLPFTIPELVHASPCRSSDGVFYT   ERN2_homSa  .....................F..   ERN1_homSap  KLPFTIPELVQASPCRSSDGILYM  CG Human
ERN2_panTro  KLPFTIPELVHASPCRSSDGVFYT   ERN2_panTr  .....................F..   ERN1_panTro  KLPFTIPELVQASPCRSSDGILYM  CG Chimp
ERN2_ponAbe  KLPFTIPELVHASPCRSSDGVFYT   ERN2_ponAb  .....................F..   ERN1_ponAbe  KLPFTIPELVQASPCRSSDGILYM  -- Gorilla
ERN2_rheMac  KLPFTIPELVHASPCRSSDGVFYT   ERN2_rheMa  .....................F..   ERN1_rheMac  KLPFTIPELVQASPCRSSDGILYM  CG Orangutan
ERN2_calJac  KLPFTIPELVHASPCRSSDGVFYT   ERN2_calJa  .....................F..   ERN1_calJac  KLPFTIPELVQASPCRSSDGILYM  CG Rhesus
ERN2_tarSyr  KLPFTIPELVHASPCRSSDGVFYT   ERN2_tarSy  .....................F..   ERN1_tarSyr  KLPFTIPELVQASPCRSSDGILYM  CG Marmoset
ERN2_micMur  KLPFTIPELVHASPCRSSDGVFYT   ERN2_micMu  .....................F..   ERN1_micMur  KLPFTIPELVQASPCRSTDGILYM  CG Tarsier
ERN2_tupBel  KLPFTIPELVHASPCRSSDGVFYT   ERN2_tupBe  .....................F..   ERN1_otoGar  KLPFTIPELVQASPCRSSDGILYM  CG Mouse_lemur
ERN2_musMus  KLPFTIPELVHASPCRSSDGVFYT   ERN2_musMu  .....................F..   ERN1_tupBel  KLPFTIPELVQASPCRSSDGILYM  -- Bushbaby
ERN2_ratNor  KLPFTIPELVHASPCRSSDGVFYT   ERN2_ratNo  .....................F..   ERN1_musMus  KLPFTIPELVQASPCRSSDGILYM  CG TreeShrew
ERN2_cavPor  KLPFTIPELVHTSPCRSSDGVFYT   ERN2_cavPo  ...........T.........F..   ERN1_ratNor  KLPFTIPELVQASPCRSSDGILYM  CG Mouse
ERN2_speTri  KLPFTIPELVHASPCRSSDGVFYT   ERN2_speTr  .....................F..   ERN1_dipOrd  KLPFTIPELVQASPCRSSDGILYM  CG Rat
ERN2_oryCun  KLPFTIPELVHASPCRSSDGVFYT   ERN2_oryCu  .....................F..   ERN1_cavPor  KLPFTIPELVQASPCRSSDGILYM  -- Kangaroo_rat
ERN2_ochPri  KLPFSIPELVHASPCRSSDGVFYT   ERN2_ochPr  ....S................F..   ERN1_speTri  KLPFTIPELVQASPCRSSDGILYM  CG Guinea_pig
ERN2_turTru  RLPFTIPELVHASPCRSSDGVFYT   ERN2_turTr  R....................F..   ERN1_oryCun  KLPFTIPELVQASPCRSSDGILYM  CG Squirrel
ERN2_bosTau  RLPFTIPELVHASPCRSSDGVFYT   ERN2_bosTa  R....................F..   ERN1_vicPac  KLPFTIPELVQASPCRSSDGILYM  CG Rabbit
ERN2_equCab  KLPFTIPELVHASPCRSSDGVFYT   ERN2_equCa  .....................F..   ERN1_turTru  KLPFTIPELVQASPCRSSDGILYM  CG Pika
ERN2_felCat  RLPFTIPELVHASPCRSSDGVFYT   ERN2_felCa  R....................F..   ERN1_bosTau  KLPFTIPELVQASPCRSSDGILYM  -- Alpaca
ERN2_canFam  KLPFTIPELVHASPCRSSDGVFYT   ERN2_canFa  .....................F..   ERN1_equCab  KLPFTIPELVQASPCRSSDGILYM  CG Dolphin
ERN2_myoLuc  KLPFTIPELVHASPCRSSDGVFYT   ERN2_myoLu  .....................F..   ERN1_canFam  KLPFTIPELVQASPCRSSDGILYM  CG Cow
ERN2_eriEur  KLPFTVPELVHTSPCRSSDGVFYT   ERN2_eriEu  .....V.....T.........F..   ERN1_myoLuc  KLPFTIPELVQASPCRSSDGILYM  CG Horse
ERN2_sorAra  KLPFTIPELVHASPCRSSDGVFYT   ERN2_sorAr  .....................F..   ERN1_pteVam  KLPFTIPELVQASPCRSSDGILYM  CG Cat
ERN2_loxAfr  KLPFTIPELVHASPCRSSDGVFYT   ERN2_loxAf  .....................F..   ERN1_eriEur  KLPFTIPELVQASPCRSSDGILYM  CG Dog
ERN2_echTel  KLPFTIPELVLASPCRSSDGVFYT   ERN2_echTe  ..........L..........F..   ERN1_sorAra  KLPFTIPELVQASPCRSSDGILYM  CG Microbat
ERN2_dasNov  KLPFTIPELVHTSPCRSSDGIFYT   ERN2_dasNo  ...........T........IF..   ERN1_loxAfr  KLPFTIPELVQASPCRSSDGILYM  -- Megabat
ERN2_monDom  KLPFTIPELVHASPCRSSDGVLYT   ERN2_monDo  KLPFTIPELVHASPCRSSDGVLYT   ERN1_proCap  KLPFTIPELVQASPCRSSDGILYM  CG Hedgehog
ERN2_macEug  KLPFTIPELVHASPCRSSDGVFYT   ERN2_macEu  .....................F..   ERN1_echTel  KLPFTIPELVQASPCRSSDGILYM  CG Shrew
ERN2_sarHar1 KLPFTIPELVQASPCRSSDGIFYM   ERN2_sarHa  ..........Q.........IF.M   ERN1_dasNov  KLPFTIPELVQASPCRSSDGILYM  -- Elephant
ERN2_sarHar2 KLPFTIPELVQASPCHSSDGIFYM   ERN2_sarHa  ..........Q....H....IF.M   ERN1_choHof  KLPFTIPELVQASPCRSSDGILYM  -- Rock_hyrax
ERN2_ornAna  KLPFTIPELVQSSPCRSSDGILYT   ERN2_ornAn  ..........QS........I...   ERN1_monDom  KLPFTIPELVQASPCRSSDGILYM  CG Tenrec
ERN2_anoCar  KLPFTIPELVQSSPCRSSDGIIYT   ERN2_anoCa  ..........QS........II..   ERN1_ornAna  KLPFTIPELVHASPCRSSDGILYM  CG Armadillo
ERN2_taeGut  KLPFTIPELVQSSPCRSSDGVLYT   ERN2_taeGu  ..........QS............   ERN1_galGal  KLPFTIPELVQASPCRSSDGILYM  CG Opossum
ERN2_galGal  KLPFTIPELVQASPCRSSDGILYM   ERN2_galGa  ..........Q.........I..M   ERN1_taeGut  KLPFTIPELVQASPCRSSDGILYM  CG Platypus
ERN2_xenTro  KLPFTIPELVQSSPCRSSDGILYT   ERN2_xenTr  ..........QS........I...   ERN1_anoCar  KLPFTIPELVQASPCRSSDGILYM  CG Lizard
ERN2_xenLae  KLPFTIPELVQSSPCRSSDGILYT   ERN2_xenLa  ..........QS........I...   ERN1_xenTro  KLPFTIPELVQSSPCRSSDGILYT  CG Tetraodon
ERN2_tetNig  KLPFTIPELVQASPCRSSDGVLYM   ERN2_tetNi  ..........Q............M   ERN1_tetNig  KLPFTIPELVQASPCRSSDGVLYM  CG Fugu
ERN2_takRub  KLPFTIPELVQASPCRSSDGVLYM   ERN2_takRu  ..........Q............M   ERN1_takRub  KLPFTIPELVQASPCRSSDGVLYM  CT Stickleback
ERN2_gasAcu  KLPFTIPDLVQSAPCRSSDGILYT   ERN2_gasAc  .......D..QSA.......I...   ERN1_gasAcu  KLPFTIPELVQASPCRSSDGVLYM  CT Medaka
ERN2_oryLat  KLPFTIPELVQSAPCRSSDGILYT   ERN2_oryLa  ..........QSA.......I...   ERN1_oryLat  KLPFTIPELVQASPCRSSDGVLYM  CG Lamprey
ERN2_calMil  KLPFTIPELVQSSPCRSSDGILYT   ERN2_calMi  ..........QS........I...   ERN1_danRer  KLPFTIPELVQASPCRSSDGILYM  
ERN2_petMar  KLPFTIPELVHASPCRTSDGVLYT   ERN2_petMa  ................T.......    
ERN_braFlo   KLPFTIPELVNASPCKSSDGILYT   ERN_braFlo  ..........N....K....I...

Case of MGAT5

chr4_4859 MGAT5 12 
>contig00001  length=538   numreads=5 21 C=2(61) Y=2(56)
LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE
.................................................
                     ^
Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in two
tasmanian  devil (here one is identical and the other differs from Monodelphis by C->Y) and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler).

Pseudogene issues: No processed pseudogenes relevent to this exon are seen by Blat of human and opossum sequence. Some questionable sequence occurs in tarsier and sloth but may be due to low coverage read or assembly error. These fragmentary sequences also have cysteine at the position in question.

Paralog issues: This gene has a moderately similar paralgog, MGAT5B, with a similar enzymatic role (beta1,6-N-acetylglucosaminyltransferase). The opossum MGAT5B protein differs at 12 positions out of 49 from opossum MGAT5, whereas human and marsupial MGAT5A differ at one residue. Consequently the two paralogs are readily distinguished within vertebrates. This is moot because 33 of 33 available MGAT5B also have cysteine at the position in question (data not shown).

Homoplasy (recurrent mutation) issues: The alignments below show tyrosine has never replaced cysteine in any other species. This cysteine is extremely invariant in both paralogs, tracing back to lophotrochozoa and cnidaria.

Known variations: No human disease alleles have been mapped to either paralog. None of 9 SNP tracks at the UCSC browser show human variatin in this exon.

Side issues: The column marked with an asterisk in the difference alignment below indicates a non-conservative phyloSNP K-->I that occured in the theran mammal stem after platypus divergence. All three marsupial sequences including tasmanian devil have isoleucine in this position as do all 30 of the available placental mammal sequences, suggesting that both the lysine and the isoleucine continue to be under strong selection. No comparable shift occured in the theran stem for MGAT5B where the residue is arginine in all species, a basic residue similar to lysine.

Structural significance: The MGAT5 gene encodes a conventional enzyme, mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, a glycosyltransferase involved in the synthesis of protein-bound and lipid-bound oligosaccharides. Surprisingly, no determined 3D structure exists at PDB at this time that is relevent to the configuration of this exon -- nor indeed the 741 residue protein. Only small regions of the protein have a prediction at ModBase.

SwissProt does not annotate the cysteine at position 532 as part of a disulfide or active site; the predicted location (Golgi) can have homodimer disulfides of similar enzymes, though this is a complex topic. Highest MGAT5 expression occurs in brain, heart, kidney, and placenta. No domains other than a signal peptide and 6 of its own glycosylation target sites are found by online tools such as SMART.

Although the bulky tyrosine substitution is conservative in the sense of polar nature and perhaps hydrogen-bonding capacity, it cannot replace these specialized functions of cysteine. Considering the extreme conservation of this cysteine, this substitution must have a substantial-- perhaps even disabling -- impact on enzymatic function.

Functional significance: In view of the facial tumor situation in tasmanian devils, OMIM's account of prior research in mouse on this gene is quite interesting. Less is known about MGAT5B though it also functions in the synthesis of complex cell surface N-glycans.

" Malignant transformation is accompanied by increased beta-1,6-GlcNAc branching of N-glycans attached to Asn-X-Ser/Thr sequences in mature glycoproteins... The amount of MGAT5 products correlates with disease progression... Mgat5-deficient mice, which are born healthy but develop various abnormalities as adults...Mgat5-deficient mice showed kidney autoimmune disease, enhanced delayed-type hypersensitivity, and increased susceptibility to experimental autoimmune encephalomyelitis...The Golgi enzyme beta1,6 N-acetylglucosaminyltransferase V (Mgat5) is up-regulated in carcinomas and promotes the substitution of N-glycan with poly N-acetyllactosamine, the preferred ligand for galectin-3 (Gal-3)...inhibitors of MGAT5 might be useful in the treatment of malignancies by targeting their dependency on focal adhesion signaling for growth and metastasis."

                                   ^                                                  ^                   *
MGAT5_homSap  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  homSap
MGAT5_panTro  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  panTro
MGAT5_gorGor  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  gorGor
MGAT5_ponAbe  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  ponAbe
MGAT5_rheMac  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  rheMac
MGAT5_calJac  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  calJac
MGAT5_micMur  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  micMur
MGAT5_otoGar  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  otoGar
MGAT5_tupBel  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  tupBel
MGAT5_musMus  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  musMus
MGAT5_ratNor  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  ratNor
MGAT5_criGri  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  criGri
MGAT5_dipOrd  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  dipOrd
MGAT5_cavPor  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  cavPor
MGAT5_speTri  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  speTri
MGAT5_oryCun  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  oryCun
MGAT5_ochPri  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  ochPri
MGAT5_vicPac  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  vicPac
MGAT5_susScr  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  susScr
MGAT5_turTru  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  turTru
MGAT5_bosTau  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  bosTau
MGAT5_equCab  LFAGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  ..A..............................................  equCab
MGAT5_felCat  lfvgLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  felCat
MGAT5_canFam  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  canFam
MGAT5_myoLuc  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  myoLuc
MGAT5_eriEur  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  eriEur
MGAT5_sorAra  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  sorAra
MGAT5_loxAfr  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  loxAfr
MGAT5_proCap  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  proCap
MGAT5_echTel  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  echTel
MGAT5_monDom  LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  monDom
MGAT5_macEug  LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  macEug
MGAT5_sarHar1 LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  sarHar1
MGAT5_sarHar2 LFVGLGFPYEGPAPLEAIANGYAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  sarHar2
MGAT5_ornAna  LFVGLGFPYEGPAPLEAIANGCAFLNLKFNPPKSSKNTDFFKGKPTLRE  ..........................L..............K.......  ornAna
MGAT5_galGal  LFVGLGFPYEGPAPLEAIANGCAFLNLRFNPPKSSKNTEFFKGKPTLRE  ..........................LR..........E..K.......  galGal
MGAT5_taeGut  LFVGLGFPYEGPAPLEAIANGCAFLNLRFNPPKSSKNTDFFKGKPTLRE  ..........................LR.............K.......  taeGut
MGAT5_anoCar  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFKGKPTLRE  .........................................K.......  anoCar
MGAT5_xenTro  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSRNTDFFKGKPTLRE  ...................................R.....K.......  xenTro
MGAT5_tetNig  VFVGLSFPYEGPAPLEALANGCIFLNPRLKPPQSSLNSEFFKEKPNIRE  V....S...........L....I....RLK..Q..L.SE..KE..NI..  tetNig
MGAT5_takRub  LFVGLSFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFKGKPTLRE  .....S...................................K.......  takRub
MGAT5_gasAcu  LFVGLSFPYEGPAPLEAIANGCAFLNPKFSPAKSSKNTDFFKGKPTLRE  .....S.......................S.A.........K.......  gasAcu
MGAT5_oryLat  LFVGLSFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFKGKPTLRE  .....S...................................K.......  oryLat
MGAT5_danRer  LFVGLSFPYEGPAPLEAIANGCAFLNPRFDPAKSSKNTDFFKGKPTLRE  .....S.....................R.D.A.........K.......  danRer
MGAT5_oncMyk  LFVGLSFPYEGPAPLEAIANGCAFLNPKFTPPKSSKNTDFFKGKPTLRE  .....S.......................T...........K.......  oncMyk
MGAT5_pimPro  LFVGLSFPYEGPAPLEAIANGCAFLNPRFDPSKSSKNTDFFKGKPTLRE  .....S.....................R.D.S.........K.......  pimPro
MGAT5_calMil  LFVGLGFPYEGPAPLEAIANGCAFLNPRFNPPKSSKNTEFFKGKPTLRE  ...........................R..........E..K.......  calMil
MGAT5_petMar  LFVGLGFPYEGPAPLEAIANGCVFLNPRFRPPKSSKNTDFFKGKPTLRE  ......................V....R.R...........K.......  petMar
MGAT5_braFlo  LFVGLGFPYEGPAPLEAIASGCVFLNPKFTQPKSRLNTKFFEGKPTFRE  ...................S..V......TQ...RL..K..E....F..  braFlo
MGAT5_strPur  LFIGLGFPYEGPAPLEAVANGCVFLNPKFNPPKNYQNTKFFQGKPTSR.
MGAT5_helRob  LFIGLGFPYEGPAPLEAIAAGCVFINPKFNPPHSSLNTKFFKGKPTARE
MGAT5_nemVec  VFIGLGFPYEGPAPLEAIQSGCVFLNAKFDPPHDRVNTPFFKNKPTLRK
MGAT5_acrMil  VFIGLGFPYEGPAPLEVISQGCVFLNPKFEPPLSSSNSDFF........

Note: the species with unfamiliar genSpp acronyms are Cricetulus griseus, Oncorhynchus mykiss, Pimephales promelas , Callorhinchus milii, Branchiostoma floridae, Strongylocentrotus purpuratus, Helobdella robusta, Nematostella vectensis, and Acropora millepora.

Case of ACTL6B

chr2_18546 ACTL6B 11  
>contig00001 length=502 numreads=11
GLSGNTMLGVGHVVTTSIGMCDIDIRP
...........................
   ^
3 G=4(94) R=7(213)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Structural significance:

Functional significance:

(more shortly)

Case of IPO7

chr5_9037 IPO7 23 
>contig00001  length=680   numreads=8
SSQVEKHSCSLTEELGSDEDDIDEDGQEYLEILAKQAGEDGDDEEWEEDDAEETALEGYSTIIDDEENPVDEYQIFKAIFQ
....*N.....................................................F.....................
                                                           ^
59 F=2(72) S=3(53)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Case of WDFY3

chr5_2532 WDFY3 19
>contig00001  length=482   numreads=8
DDFSEESSFYEILPCCARFRCGDLIVEGQWHHLVLVMSKGMLKNSTAALYIDGQLVSTVK
................T..............................T..L.....N...
                ^
16      T=3(117)        A=5(138)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Structural significance:

Functional significance:

(more shortly)

Case of PPFIA3

chr4_22002 PPFIA3 15  incorrectly mapped from monDom5 to human
>contig00001  length=298   numreads=4
LIQEEKETTEQRAEELESRVSGSGLDSLGRYRASCSLPPSLTTSTLASPSPPSSGHSTPRPAPPSPAREAPANSTSNTAEKP
........................................................F..................G.V.
                                                        ^
 56 F=2(43) S=2(37)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Structural significance:

Functional significance:

(more shortly)

Structural significance:

Functional significance:

(more shortly)

Other cases to be considered

chr6_2360 XYLT1 5  61 D=3(110) A=5(107)
>contig00001  length=488   numreads=10
RSNYMHRQVLQFAGQYQNVRVTSWRMATIWGGASLLSTYLQSMRDLMEMTDWPWDFFINLSAADYPI
 ...L........................................................D.....
                                                             ^

chr4_18550 ATP4A 6 16 C=4(130) R=3(74)
>contig00001  length=906   numreads=10
TAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVT
................C........................................................................
                ^

chr4_11174 FLI1 3  32 N=2(63) K=3(47)
>contig00001  length=575   numreads=9
ESPVDCSVNKCSKLVGGNESNPMNYNTYMDEKNGPPPNMTTNERRVIVPA
..................................................
                                ^

chr2_30280 VPS72 5  15 R=3(59) K=2(51)    
>contig00001  length=591   numreads=6
NYERLEADKKKQVHKKRKCPGPVITYHSMTVPLLAEPGPKEENVDVE
...............R..................T............
               ^

chr6_5144 ABCC1 23  4 Q=2(69) P=2(80) looks like a frame-shift problem in monDom5
>contig00001  length=802   numreads=10
HLCFPRLHLDLLHNVLRSPMSFFERTPSGNLVNRFSKEMDTVDSMIPQIIKMFMGSLFNVIGACIIILLATPIAAIIIPPLGLIYFFVQ
....Q....................................................................................
    ^

chr5_8347 SPON1 11  20 V=3(65) I=2(66) wobbly
>contig00001  length=433   numreads=5
GSTCTMSEWITWSPCSISCGVGMRSRERYVKQFPEDGSVCTVPTEETEKCTVNEEC
......................................I.N...............
                    ^

chr3_5872 ACOT12 14 14 I=3(95) V=3(110) wobbly
>contig00001  length=472   numreads=6
NTYVVAVKSVTLASIPPSPQYNRSEITCAGFLIRAVDSNSCT
.................................Q....S...
              ^

Other marsupial genes of interest

The collections below contain well-understood genes with very extensive comparative genomics. They can serve as a test bed for Sarcophilus assembly quality, a place where genuine anomalies or distinct adaptive features might surface (perhaps as phyloSNPs) and where marsupial phylogeny might be refined using rare genomic events in nuclear genes.

The gene sets contain all available marsupial orthologs plus for context one flanking gene each from placentals and monotremes. These genes are available in much broader hand-curated sets elsewhere on this site.

Rod rhodopsin RHO1 (4 marsupials)

The optimal wavelength for scotopic (dim light) vision of Sarcophilus is easily predictable provided key tuning residues are covered by the assembly.

>RHO1_homSap Homo sapiens (human)   
0 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG 1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 2
1 YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 0
0 FRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA* 0

>RHO1_monDom Monodelphis domesticus (opossum) Didelphimorphia
0 MNGTEGPNFYVPFSNKTGTVRSPFEEPQYYLADPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTMTLYTSLHGYFVFGPTGCNLEGFFATLG 1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIIGVAFTWVMALACAFPPLIGWSR 2
1 YIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTIPAFFAKSSSVYNPVIYIMMNKQ 0
0 FRTCMITTLCCGKNPLGDDEASATASKTETSQVAPA* 0

>RHO1_macEug Macropus eugenii (wallaby) Diprotodontia frag, traces not yet consulted
0 MNGTEGPNFYVPFSNKTGVVRSPFEEPQYYLAEPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLADADLFMDFGGFT       1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACSTPPLLGWSR 2
1 0
0       ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKTSAVYNPVIYIMMNKQ 0
0 FRNCMITTLCCGKNPLGDDEASATTSKTETSQVAPA* 0

>RHO1_smiCra Sminthopsis crassicaudata (fat-tailed dunnart) Dasyuromorphia
MNGTEGPNFYVPYSNKSGVVRSPYEEPQYYLAEPWMFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAVADLFMVICGFTTTLVTSLNGY
FVFGTTGCLVEGFFATTGGEVALWALVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACSVPPIFGWSRYIPEGMQCSCGIDYYTLNPEFNNESFVIYMFVVHFIIPLTV
IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSDFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMITTLCCGKNPLGDDEASTTASKTETSQVAPA*

>RHO1_calPhi Caluromys philander (woolly opossum) Didelphimorphia abstract:14659889
MNGTEGPNFYVPFSNKTGVVRSPFEEPQYYLAEPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTTTLYTSLHGY
FVFGPTGCDLEGFFATLGGEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMVV
IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPILMTLPAFFAKTSAVYNPVIYIMLNKQFRTCMLTTLCCGKIPLGDDEASATASKTETSQVAPA*

>RHO1_ornAna Ornithorhynchus anatinus (platypus) 
0 MNGTEGQDFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSVLAAYMFMLIMLGFPINFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVLGGFTTTLYTSLHGYFVFGPTGCNIEGFFATLG 1
2 GEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACALPPLVGWSR 2
1 YIPEGMQCSCGIDYYTLRPEVNNESFVIYMFVVHFTIPMTIIFFCYGRLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTVPAFFAKSSAIYNPVIYIMMNKQ 0
0 FRNCMLTTICCGKNPLGDDEASATASKTEQSSVSTSQVSPA* 0

Cone rhodopsin SWS2 (9 marsupials)

Cone rhodopsin RHO2 has been lost in all mammals and no debris from this gene is expected in Sacrophilus). The short wavelength cone opsin SWS2, while still present in platypus, has also been lost in all theran opsion too long ago to leave detectable remnants in syntenic position. Cone opsin SWS1 has this turned around, being present in theran mammals but only as debris in platypus.

>SWS1_homSap Homo sapiens (human) Gt 0.2.2.1.0.0 indel -FAM137A -CALU -NAG6 -FLNC 348 aa 000 nm 1385866 NP_990769 cone short   
0 MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVA 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNPIIYCFMNKQ 0
0 FQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN* 0

>SWS1_monDom Monodelphis domesticus (opossum) Didelphimorphia
0 MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHFQTVFMGFVFCAGTPLNAVVLVATLRYKKLRQPLNYILVNVSLCGFIFCIFAVFTVFISSSQGYFIFGRHVCAMEAFLGSVA 1
2 GLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWVIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIMPLFLICFSYSQLLRALRA 0
0 VAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNQNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FHACIMEMVCRKPMTDDSDVSSSQKTEVSAVSSSQVGPT* 0

>SWS1_thyEle Thylamys elegans (fat-tailed opossum) Didelphimorphia 
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHLQTVFMGFVFC
AGTPLNAVVLVATLRYKKLRQPLNYILVNVSFSGFIFCIFAVFTVFISSSQGYFIFGH
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWVIGI
GVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLFLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMVCRKPMTDDSDVSSSQKTE
VSAVSSSQVGPS

>SWS1_didAur Didelphis aurita (big-eared opossum) Didelphimorphia
MSGDEEFYLFKNISSVGPWDGPQHHIAPAWAFHFQTVFMGFVFC
AGTPLNAVVLVATLRYKKLRQPLNYILVNVSLSGFIFCIFAVFTVFISSSRGYFVFGR
HVCAMEAFLGSVAGLVMGWSLAFLAFERFVVICKPFGNFRFNAKHAMMVVLATWVIGI
GVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSEYYAWFLFLSCFIGPLFLICFSY
AQLLGALRAVAAQQQESTTTQKAEREVSRMVVMMVGSFCLCYVPYAALGMYMINNRNH
GLDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMVCRKPMADDSDITSSQKTE
VSTVSSSQVGPS

>SWS1_macEug Macropus eugenii (wallaby) Diprotodontia
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHCQTVFMGFVFFAGTPLNAVVLIATFRYKKLRQPLNYILVNISLAGFIYCIFSVFTVFISSSQGYFIFGR
HVCAMEGFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFNSKHSMMVVLATWVIGIGVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFILCFIMPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNRNHGIDLRLVTIPAFFSKSSCVYNPIIYCFMNKQFHACIMEMVCRKPMTDDSEASSSQKTEVSTVSSSQVGPS*

>SWS1_setBra Setonix brachyurus (quokka) Diprotodontia 
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHCQTVFMGFVFF
AGTPLNAVVLIATFRYKKLRQPLNYILVNISLAGFIYCIISVFTVFISSSQGYFIFGR
HVCAMEGFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFNSKHSMMVVLATWVIGI
GVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYHSEYYTWFLFILCFIMPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNRNH
GIDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMVCRKPMTDDSEASSSQKTE
VSTVSSSQVGPS

>SWS1_tarRos Tarsipes rostratus (honey possum) Diprotodontia
MSGDEEFYLFKDISSVGPWDGPQYHIAPAWAFHFQTTFMGFVFF
AGTPLNAVVLIATLRYKKLRQPLNYILVNISLAGFIFCVISVFTVFISSSQGYFIFGR
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFSSKHAMMVVLATWVIGI
GVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYHSEYYTGFLFIFCFIVPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPAFFSKSACVYNPIVYWFMNKQFHACIMEMVCRKPMTDDSEISSSQKTE
VSTVSSSQVGPS

>SWS1_cerCon Cercartetus concinnus (pygmy possum) Diprotodontia
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHFQTAFMGFVFF
VGTPLNAVVLVATLCYKKLRQPLNYILVNVSLAGFIFCIISVFTVFISSSQGYFIFGR
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFSSKHAMMVVLATWVIGI
GVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPACFSK 

>SWS1_smiCra Sminthopsis crassicaudata (dunnart) Dasyuromorphia
0 MSGDEEFYLFKNISLVGPWDGPQYHLAPAWAFHFQTAFMGFVFFAGTSLNGVVLIATLRYKKLRQPLNYILVNISLAGFIFCVFSVFTVFVSSSQGYFVFGRHVCAMEGFLGSVA 1
2 GLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWIIGIGVSIPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLICFSYSQLLGALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAAMAMYMVNNRNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FHACIMEMICKKPMTDDSETTSSQKTEVSTVSSSQVGPS* 0
 
>SWS1_isoObe Isoodon obesulus (bandicoot) Peramelemorphia
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHCQTVFMGFVFF
AGTPLNAVVLIATLRYKKLRQPLNYILVNISLAGFIFCIFSVFTVFISSSQGYFIFGR
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFHSKHAMMVVLATWVIGI
GVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIIPLSLICFSY
SQLLRALRTVAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMICRKPMTDDSETSSSQKTE
VSTVSSSQVSPS

>SWS1_galGal Gallus gallus (chicken) Gt 0...2.1.0.0 indel x x x x 348 aa 000 nm no_ref genome cone short1 violet   
0 MSSDDDFYLFTNGSVPGPWDGPQYHIAPPWAFYLQTAFMGIVFAVGTPLNAVVLWVTVRYKRLRQPLNYILVNISASGFVSCVLSVFVVFVASARGYFVFGKRVCELEAFVGTHG 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFSSRHALLVVVATWLIGVGVGLPPFFGWSR 2
1 YMPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLIIFSYSQLLSALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRDHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FRACIMETVCGKPLTDDSDASTSAQRTEVSSVSSSQVGPT* 0

Cone rhodopsin LWS (9 marsupials)

This basal imaging opsin is available from 97 vertebrates and has already been analyzed for phyloSNPs and rare genomic events. The Didelphimorphia experienced a 3-4 residue insert in exon 1 that separates them from all other marsupials. Note this region has quite a complicated indel history. The extra residues have repeat character DVNE DDND suggesting replication slippage.

LWS_loxAfr  MAQQWGPHRLTGARLQDASE---DSTQASIFVYTNTNT  elephant
LWS_echTel  MAQRWGAHRLTGGQLQDTYE---GSTRTSIFVYTNSTS  tenrec
LWS_monDom  MTQAWDPAGFLARRRDVNEDDNDETTRSSLFVYTNSNN Didelphimorphia
LWS_didAur  MTQAWDPVGFLARRRDENEDDHDDTTRASLFVYTNSNN Didelphimorphia
LWS_tarRos  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_macEug  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_smiCra  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Dasyuromorphia
LWS_setBra  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_cerCon  MTQAWDPAGFLAWQEDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_myrFas  MTQAWDPAGFLAWRREENE----ETTRASLFTYTNSNN Dasyuromorphia
LWS_isoObe  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Peramelemorphia
LWS_ornAna  MTPAWNSGVYAARRRFEDEE---DTTRTSVFVYTNSNN  platupus
LWS_tacAcu  MTQAWDPAGFLAWRRDENEE---TTRASLFVYTNSNNT  echidna

>LWS_homSap Homo sapiens (human)   
0 MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTR 1
2 GPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFVLGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRA 0
0 VAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVIYVFMNRQ 0
0 FRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA* 0

>LWS_monDom Monodelphis domesticus (opossum) Didelphimorphia 4aa insert  
0 MTQAWDPAGFLARRRDVNEDDNDETTRSSLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETVIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMATCCIFPLSIILLCYVQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYSFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSKTEGSSVSSVAPA* 0

>LWS_didAur Didelphis aurita (big-eared opossum) Didelphimorphia 4aa insert
0 MTQAWDPVGFLARRRDENEDDHDDTTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETVIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAAVWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDLGVQSYMIVLMATCCIFPLSIILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSKTEVSSVSSVAPA* 0

>LWS_tarRos Tarsipes rostratus (honey possum) Diprotodontia ENED insert
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVFNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAIWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGIQSYMIVLMSTCCILPLSIILLCYVQVWRAIRA 2
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_macEug Macropus eugenii (wallaby) Diprotodontia  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVFNLTSLWMIFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGVQSYMIVLMSTCCILPLSVIFLCYIQVWLAIRS 2
0 VAKQQKESESTQKAEKEVSRMVVVMILAFCFCWGPYAIFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_setBra Setonix brachyurus (quokka) Diprotodonti  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVFNLTSLWMIFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETMIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGVQSYMIVLMSTCCILPLSVILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYAIFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVPA* 0

>LWS_cerCon Cercartetus concinnus (pygmy possum) Diprotodontia 
0 MTQAWDPAGFLAWQEDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVFNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAIADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAIWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGIQSYMIVLMSTCCILPLSIILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTFFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA*

>LWS_smiCra Sminthopsis crassicaudata (dunnart) Dasyuromorphia
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVYNLTSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIILCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVMVMILAFCFCWGPYALFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_myrFas Myrmecobius fasciatus (numbat) Dasyuromorphia
0 MTQAWDPAGFLAWRREENEETTRASLFTYTNSNNTK 1
2 GPFEGPNYHIAPRWVYNLTSFWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSVILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYAIFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_isoObe Isoodon obesulus (bandicoot) Peramelemorphia  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSFWMFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMTTCCILPLSIILLCYVQVWLAIRA 0
0 VAKQQKDSESTQKAEKEVSRMVVVMIRAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSGTSRTEVSSVSSAPA* 0

>LWS_ornAna Ornithorhynchus anatinus (platypus)  
0 MTPAWNSGVYAARRRFEDEEDTTRTSVFVYTNSNNTR 1
2 DPFEGPNYHIAPRWAYNVTSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLSIISWERWIVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIVLCYLQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTIFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIMQLFGKKVDDGSELSSTSRTEVSSVSSVSPA* 0

>LWS_tacAcu Tachyglossus aculeatus (echidna)  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVFNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAVWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMATCCIFPLSIILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSKTEVSSVSSVAPA* 0

Encephalopsin (2 marsupials)

Encephalopsin has a very peculiar history of gene loss in tetrapods, requiring some seven independent events. While this limits the phylogenetic utility of gene loss within marsupials, it is still of interest to determine the status of the gene within Sarcophilus.

>ENCEPH_homSap Homo sapiens (human) OPN3 
0 MYSGNRSGGHGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0


>ENCEPH_monDom Monodelphis domestica (opossum) 
0 MYSDNSSDDGGGGYWGSGRAGGASGTGVTGEPGPEGSPRQAPLFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 1
2 GIVSIMTLTVLAYERYNRIVHAKVINFSWAWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVIFLFFGCLMLPVGVMAYCYGHILYAIRM
0 LRCVEELQTIQVIKILRYEKKVAKMCFLMIAIFLFCWMPYAVICLLVANGYGSLVTPTVAIIASLFAKSSTAYNPIIYIFMSRK 0
0 FRRCLLQLLCFRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDENDKNSGTKVNVIQVRPL* 0

>ENCEPH_macEug Macropus eugenii frag
0                         GALGCREPGQREPSSSAPFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLLLVNISFSDLLVSLFGVTFTFVSCLRSGWVWHTVGCAWDGFSNSLF 1
2 GIVSIMTLTVLAYERYHRIVHAKVINFSWTWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVLFLFLGCLVLPVGVMAYCYGHILYAIRM 0
0 0
0 FRRCLLQLLCFRQLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDDNDKNNGTKVNVIQVRPL* 0

>ENCEPH_ornAna Ornithorhynchus anatinus pseudo
0 MVPWNGS-GRHLGAVR---GPE--SLPATPGAARPSRPGAGDGRL--LGLF-P-GVGGNLLVLLL--ALPGPPTTTDLYLASVAVSDLL--LL---LPFVYRLWRSRPWVFVCRLLGE-GGSLA 1
2 GIVSLISLAVLSYERYTLTLHPKQSNYQKAVLAVGASWIYSLIWTIPPLLGWSSYGTEGAGTSCSVHWSSKSVC-SYIVCLFI--CLVIPVLVMIYCYGRLLYAVKQ 0
0 LHCVKELQNIQVIGSLRYER*VTEMYFFTIAQFLVCQSPSALVSYPAAH-----VSPVVAKISPVFANSSFVYNPVISIFVRRK 0
0 KASR*KVNVIQVQPPS* 0

>ENCEPH_galGal Gallus gallus (chicken) 71%=homSap encephalopsin OPN3 full
0 MHSGNGTGATSRPQLAAAGHEVPGERPLFSAGTYELLALLIATIGTLGVCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVCGVSLTFMSCLRSRWVWDAAGCVWDGFSNSLF 1
2 GIVSIMTLTVLAYERYIRVVHAKVIDFSWSWRAITYIWLYSLAWTGAPLLGWNRYTLEIHGLGCSMDWKSKDPNDTSFVLLFFLGCLVAPVVIMAYCYGHILYAVRM 0
0 LRCVEDFQTSQVIKLLKYEKKVAKMCFLMISTFLICWMPYAVVSLLVTYGYSNLVTPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRQCLLQLLCFRLMRFQRIMKEPSGAGNVKPIRPIVMSQKVGDRPKKKVTFSSSSIIFIIASDDTQQIDDNSKHNGTKVNVIQVKPL* 0

TMT opsin (2 marsupials)

TMT is an ancient locus that is present in monotremes and marsupials but lost in all placentals.

>TMT_monDom Monodelphis domestica shortened final exon 
0 MSNNLTTNLSLEALLSASEDKQRNGLSRTGHTIVAVFLGIILIFGSISNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLSGTTLSFASSIQGRWIGGKHGCRWYGFANSCF 1
2 GIVSLISLAILSYERYRTLTLCPGQGADYQKALLAVAGSWLYSLVWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILVMVYFYGRLLYAVKQ 0
0 VGKIRKTAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYVLMNKQ 0
0 FYKCFLILFHCQPAQSGPDVSLCPSNVTVIQLGQRKNKDAPGSI*

>TMT_macEug Macropus eugenii frag
0 MSINLTANLSFGTLLPDSEEKQRSGLSRTGHTVTAVFLGLILILGVINNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLTGTTLSFASSIRGRWIAGYHGCRWYGFANSCF 1
2 GIVSLISLAVLSYERYRTLTLCPRQGTDYHKALLAVAGSWLYSLIWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILFMVYFYGRLLYTVKQ 0
0 VGKIRKSAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFLILFHCQPASSASDASLCPSKMTVIQLGQRKDKEVPCAIQDLPEVSKKQLCLLSPESNVAPSSGHPQEKMEEKPLSE*  0

>TMT_ornAna Ornithorhynchus anatinus frag
0                        GLSRTGHTMVAVFLGIILVFGFMNNLIVLILFCKFKALRNPVNMIMLNISASDMLVCVSGTTLSFASNISGRWIGGDPGCRWYGFVNSCL 1
2 GIVSLISLAVLSYERYRTLTLHPKQSTDYQKAVLAVGASWIYSLIWTIPPLLGWSSYGTEGAGTSCSVHWSSKSPVSVSYIVCLFIFCLVIPVLVMIYCYGRLLYAVKQ 0
0 IGKARKTAARKREYHVLFMVITTVICYLVCWMPYGVTALLATFGQPGTVSPEASVIPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFLILFHCQPPRAADAPSTYPSQVMVIQLNQRRSRETAGAPQVLLEMKHQTLHLLGPQLHETPSWERSTPVHPE* 0

>TMT_galGal Gallus gallus 
0 MNHTWTYNLSFGAPTDPVEPRAGLSRNGHTVVAVFLGFILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNIhttp://genomewiki.ucsc.edu/index.php?title=Opsin_evolution:_Encephalopsin_gene_loss&action=editSISDMLVCISGTTLSFASNIHGKWIGGEHGCRWYGFVNSCF 1
2 GIVSLISLAVLSYERYSTLTLCNKRSDDYRKALLAVGGSWVYSLLWTVPPLLGWSSYGIEGAGTSCSVRWSSETAESTSYIICLFIFCLVIPVMVMMYCYGRLLYAVKQ 0
0 VGKIHKNTARKREYHVLFMVITTVICYLVCWIPYGVIALLATFGKPGVVTPVASIIPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFRQLFHCQPPSSTDGEPTCHSKVTVIQLNQKTDGGKLCNNKPRPETDNKVTSLLHPEPGLEPAAKTVPPM*  0