Opsin evolution: Encephalopsin gene loss

Introduction to Encephalopsin Evolution

Encephalopsin is a pivotal ciliary opsin, with basal evolutionary position to the imaging opsin gene expansion and well represented in early diverging deuterstomes, notably the cephalochordate Branchiostoma. Despite this, encephalopsin has been the subject of just one substantive publication dating to 1999. That article primarily emphasized its non-retinal distribution in mouse brain:

"Encephalopsin is highly expressed in the preoptic area and paraventricular nucleus of the hypothalamus ... in selected regions of the cerebral cortex, cerebellar Purkinje cells, a subset of striatal neurons, selected thalamic nuclei, and a subset of interneurons in the ventral horn of the spinal cord. Rostrocaudal gradients of encephalopsin expression are present in the cortex, cerebellum, and striatum. Radial stripes of encephalopsin expression are seen in the cerebellum."

The gene is well-represented in chondrichthyes and teleost fish with multiple independent copies, but single copies in amphibians, birds, lizard, marsupials, primates and rodents, with excellent amino acid conservation (over 60% between telost fish and human). Surprisingly, upon more intensive taxonomic sampling, functional encephalopsin turns out to completely absent in a variety of other mammalian clades. While interesting in its own right, this complicates the standard application of comparative genomics to the evolution of encephalopsin structure and function.

Massive encephalopsin gene loss in mammals

The table lists 10 species that today have unprocessed pseudogenes in place of a once-functional encephalopsin gene. The observed phylogenetic distribution of loss (which is irreversible) requires a minimum of 6 independent events, for example in some bats but not others. At the level of superordinal clades, no gene loss is observed in Euarchontoglires but Laurasiatheres (especially artiodactyls) are heavily affected as well as the Xenarthra within Atlantogenata and at least platypus within monotremes.

The odd feature of these pseudogenes is that they must all have arisen fairly recent on the mammalian time scale to remain observable today as decayed relics. However they survive at variable degrees of degeneration. This suggests that the losses are not coordinated with a single unifying global environmental event.

As the function of encephalopsin is obscure, the consequences of gene loss are even more so. Encephalopsin may have lost its supporting selected function; no increase in opsin gene number has compensated for this (from homology searches of complete genomes).

The clade-incoherent gene loss of encephalopsin is reminiscent of loss of GULO, the terminal enzyme for L-ascorbic acid biosynthesis, with relic gene fragments still detectable in guinea pigs (gene estimated lost 20 myr ago) and primates (lost on stem between lemurs and tarsier about 60 myr ago). At least 5 independent losses have been documented in some passerine birds, all tested species of bats, and teleost fish from zebrafish on (but not including sturgeon, chondrichthyes, or lamprey). A 2007 study of loss of GUCYD (GPCR signaling guanyl cyclase D) exemplifies modern pseudogene dating methods.

In the table, 'ok' indicates presence of a gene with conserved sequence characteristics appropriate to functioning opsins and appropriate to the ancestral encephalopsin class; ps indicates definite pseudogenization of the 4-exon gene (reading frame shifts, internal stop codons, loss of sequence conservation in expected regions); +- indicates partial gene recovery with some uncertainty (traces commonly have errors such as short indels and quality departure at their ends; repetitive base composition in exon 1 may have lead to trace read technical problems).

ok	>ENCEPH_homSap Homo sapiens (human) NM_014322 OPN3 full
ok	>ENCEPH_panTro Pan troglodytes full
ok	>ENCEPH_gorGor Gorilla gorilla ok frag
ok	>ENCEPH_ponAbe Pongo abelii full
ok	>ENCEPH_nomLeu Nomascus leucogenys exon 1 ok frag
ok	>ENCEPH_macMul Macaca mulatta (rhesus) XP_001094239 full
ok	>ENCEPH_papHam Papio hamadryas 1st exon problematic 1x ok frag
ok	>ENCEPH_calJac Callithrix jacchus full
ok	>ENCEPH_tarSyr Tarsius syrichta
ok	>ENCEPH_micMur Microcebus murinus full
ok	>ENCEPH_otoGar Otolemur garnettii full
+-	>ENCEPH_tupBel Tupaia belangeri so-so frag
	
ok	>ENCEPH_musMus Mus musculus Opn3 Panopsin NM_010098 2aa del full
ok	>ENCEPH_ratNor Rattus norvegicus XP_573517 predicted 2aa del full
ok	>ENCEPH_speTri Spermophilus tridecemlineatus full
ok	>ENCEPH_dipOrd Dipodomys ordii full
ok	>ENCEPH_cavPor Cavia porcellus 3 aa del full
ok	>ENCEPH_oryCun Oryctolagus cuniculus full
ok	>ENCEPH_ochPri Ochotona princeps 5aa del ok frag
	
ok	>ENCEPH_canFam Canis familiaris (dog) XP_854433 full
ok	>ENCEPH_felCat Felis catus full
ps	>ENCEPH_bosTau pseudo frag
ps	>ENCEPH_turTru Tursiops truncatus pseudo frag
ps	>ENCEPH_susScro no coverage
ps	>ENCEPH_vicVic pseudo pseudo frag
ps	>ENCEPH_myoLuc Myotis lucifugus weak frag
ok	>ENCEPH_pteVam Pteropus vampyrus 86%=homSap full
ok	>ENCEPH_equCab Equus caballus full
ps	>ENCEPH_sorAra pseudo frag
ps	>ENCEPH_eriEur no coverage
	
ok	>ENCEPH_loxAfr Loxodonta africana 2 exons in browser, 1 2x full
ps	>ENCEPH_echTel Echinops telfairi no coverage
ok	>ENCEPH_proCap Procavia capensis ok frag
ps	>ENCEPH_dasNov Dasypus novemcinctus  pseudo
+-	>ENCEPH_choHof Chololepis hoffmanni so-so frag
ok	>ENCEPH_monDom Monodelphis domestica (opossum) encephalopsin OPN3 75%=homSap full
ok	>ENCEPH_macEug Macropus eugenii ok frag
ps	>ENCEPH_ornAna Ornithorhynchus anatinus pseudo
	
ok	>ENCEPH_xenTro Xenopus tropicalis (frog) 45%=homSap full 
ok	>ENCEPH_galGal Gallus gallus (chicken) 71%=homSap encephalopsin OPN3 full
ok	>ENCEPH_taeGut Taeniopygia guttata mrna CK301424 70%=homSap full
ok	>ENCEPH_anoCar Anolis carolinensis (lizard) 70%=homSap OPN3 full
	
ok	>ENCEPH_danRer Danio rerio (zebrafish) NM_001111164 mrna 61%=homSap full
ok	>ENCEPH_gasAcu Gasterosteus aculeatus (stickleback) 58%=homSap full
ok	>ENCEPH_oryLat Oryzias latipes  58%=homSap full
ok	>ENCEPH_takRub Takifugu rubripes (pufferfish) homSap=61% full

Post-marsupial loss of TMT encephalopsin

TMT (for teleost multiple tissue) is another fairly obscure opsin, again subject of but a single publication that established its expression in "a variety of neural and non-neural tissues, including a zebrafish embryonic cell line that exhibits a light entrainable clock" suggesting TMT regulates peripheral clocks in teleost fish.

We see below that orthologs are readily located in chondrichthyes, fish, frog, lizard, birds, and marsupials but once again the gene has been lost in all placental mammals even as it persists to the present day in other vertebrates, this time vanishing without a trace (suggesting by parsimony a single event on the ancestral common stem).

TMT is an encephalopsin-class opsin, clustering most closely with these opsins. Although found initially in fish, it is not the product of a whole genome duplication there because synteny is lacking, the two encephalopsins are quite diverged, and preceding and following species lacking the duplication also have both copies. Thus TMT likely arose in lamprey ancestor if not earlier. Indeed, one encephalopsin of cephalochordates aligns more with TMT than classical encephalopsins. TMT might thus be the ancestral gene, with encephalopsin a derived form receiving more emphasis historically because it persisted into some placentals, notably human, unlike TMT. The sea urchin gene associates equally with the two encephalopsin classes.

Reference set of curated encephalopsins (including pseudogenes)

>ENCEPH_homSap Homo sapiens (human) NM_014322 OPN3 full
0 MYSGNRSGGHGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_panTro Pan troglodytes full
0 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_gorGor Gorilla gorilla ok frag
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0

>ENCEPH_ponAbe Pongo abelii full
0 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLMVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVAIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGRLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_nomLeu Nomascus leucogenys exon 1 ok frag
0 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGN  1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVLMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_macMul Macaca mulatta (rhesus) XP_001094239 full
1 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_papHam Papio hamadryas 1st exon problematic 1x ok frag
0 MYSGNRSGGQGYWDGGGAAGTEGPALVGTLIPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLL LLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLFG 1
2 gIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_calJac Callithrix jacchus full
0 MYSGNRSGGQGYWDGGEAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSNLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRMLRCQQPAKDLSAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_tarSyr Tarsius syrichta weak full
0 MYSGNRSGGQGSWEGGGAAGAEGPAAAGIPAPIISRGTYERLALVLLGSIGLLGVGNNLLVLVLYYKFPRLRTPTHLLLANISLSDLLVSLFGVTFTFVSCLRNGWVWDTVDCMGYVLTIDLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDTSFVLFLFLGCLVVPMGVISYCYGHILYSIRe 0
0 LRCVEDLQTIQVIKILKYEKKVAKMCFFMIFTFLICWMPYIVICFLVVNSQGHLVTPTISVVSYLFAKSNTVYNPVIYIFMIRK 0
0 FRRSLLQFLCLRLLRCQQPAKDLPAAENEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTSGSKVDVIQVRPL* 0

>ENCEPH_otoGar Otolemur garnettii full
0 MYSGNRSGGQGFWEGGGAAGAEEPTPEGTLSPAPLFSPSAYERLALLLGSIGLLGVANNLLVLVLYYKFPRLRTPTHLFLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPVGVVAHCYGHILYSIRM 0
0 LRCVEDLQTTQVIKILKYEKKVAKMCFFMIFTFLVCWMPLIVICFLVVNGQGHLVTPTVSIVSYLLAKSNTVYNPVIYIFMLRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPAAESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDNSDKTNGSKVDVIQVRPL* 0

>ENCEPH_micMur Microcebus murinus full
0 MYSGNRSGGQWFWEGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFPRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPVGVMVHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGQRHLVTPTVSIVSYLFAKSNTVYNPIIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPASESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDNSDKTSGSKVDVIQVRPL* 0

>ENCEPH_tupBel Tupaia belangeri so-so frag
0   SGNRRGGQGLLEGGGAVGVEGLAPTGSQSPAPLFSRGTYERLALLLGSIGLLGVGHNLLVLVLYYKFPRLRTPTHLLLLNISLGDLLVSVFGVTFTFVTCLRNGWVWDTVSCAWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFPWAWRAITYIWLYSLAWAGAPLLGWNRYMLDVHGLGCTVDWKSK
0           MINILRYKKKVAKMCFLMILTFLICWMPYIVIRFLVVNGGYGHLITPTVSIVSFLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRYQRPAKDLPAAGSEMQIRPIVMSQKDGDKPKKKVTFNSSSIIFIITSDESLSVDDSDKTSGSKVDVIQVRPL* 0

>ENCEPH_musMus Mus musculus Opn3 Panopsin NM_010098 2aa del full
0 MYSGNRSGDQGYWEDGAGAEGAAPAGTRSPAPLFSPTAYERLALLLGCLALLGVGGNLLVLLLYSKFPRLRTPTHLFLVNLSLGDLLVSLFGVTFTFASCLRNGWVWDAVGCAWDGFSGSLF 1
2 GFVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLGCTVDWRSKDANDSSFVLFLFLGCLVVPVGIIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKMLRYEKKVAKMCFLMAFVFLTCWMPYIVTRFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMNRK 0
0 FRRSLLQLLCFRLLRCQRPAKNLPAAESEMHIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDSDRSSASKVDVIQVRPL* 0

>ENCEPH_ratNor Rattus norvegicus XP_573517 predicted 2aa del full
0 MYSGNRSGGQGYWEDGAGAEGAAPAGTRSPAPLFSPTAYERLALLLGCLALLGVGGNLLVLLLYSKFPRLRTPTHLFLVNLSLGDLLVSLFGVTFTFASCLRNGWVWDAVGCAWDGFSGSLF 1
2 GFVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPMGIIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKMLRYEKKVAKMCFLMAFVFLTCWMPYVVTRFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKNLPAAESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDSDRSSASKVDVIQVRPL* 0

>ENCEPH_speTri Spermophilus tridecemlineatus full
0 MYSGNRSGSQGSWEGDGSAGAEGSAPEGTLSPTPLFSPGTNERLALLFRSVGLLGAGSNLLVLVLYYKFQGSAHPLTFFLVNISLGDLLMSLFGVTFTFVSCLRNRWVWDTVACVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVEWKSKDANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSIRM 0
0 LRCVEDLQIFQVIKILRYEKKLAKMCFVMVFTFLICWMPYIVVCFLVANGYGQRVTPTVSIVSNLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCSRLLRCQQPAKDLPAVGNEMQIRPIVISQKDGERPKKKVTFNSSSIVFIITSDESLSVDDSNRTSGSKADVIQVRPL* 0

>ENCEPH_dipOrd Dipodomys ordii full
0 MYSGNRSGGQEYWEDGGAAGSEGPAPAGTLSPAPLFSAGAYERLALLLGSAGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSRSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFTWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLGCTVDWKAKDANDSSFVLFLFIGCLVVPVGIIAHCYGHILYSIRM 0
0 LRCVEDLQTIQIIKILQYEKKLAKMCFLMALTFLMCWMPYIVTCFLVVNSHGHLVTPTISIVSHLLAKSSTIYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSVRSSGSKADVIQVRPL* 0

>ENCEPH_cavPor Cavia porcellus 3 aa del full
0 MYSGNRSSGQGYWEGGGPEDPAPAGTLSPAPLFSPGAYERLALLLGSLGLLGVGNNLLVLVLYYKFQRLRSPTHLFLANISLSDLLGSLFGVTFTFVSCLKNGWVWDAVGCVWDGFSRSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLSCTVDWKSKDANDSSFVLFLFLGCLVVPVGVIVHCYGHILYSIRM 0
0 LRGVEDLQTIQVMKILRSENKVAIMCFLMVFIFLVCWMPYIVICFLLVNGYRHRVTPTVSIVSYLFTKSSTVYNPVIYVLMIRK 0
0 FRRSLLQLHCLRLLRCQQPAKDLPAVEREMHIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDRTSGSKVDTIQVRPL* 0

>ENCEPH_oryCun Oryctolagus cuniculus full
0 MYSGNRSGEQGYWEGGGAAGAEGPGPAGTLSPAPLFSPSTYERLALLLGSIGLLGVGSNLLVLVLYYKFQRLRTPTLLFLVNISLSDLLVSVFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLGCTVDWKSKNANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFFMVFTFLICWMPYVVICFLVVNGYGHLVTPTLSIVSYLFCKSSTAYNPIIYIFMIRK 0
0 FRRSLLQLLCFQPLRCQQPPKDLPTVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIIASDESLAVDDNEKASGPKVDVIQVRPL* 0

>ENCEPH_ochPri Ochotona princeps 5aa del ok frag
0 MYSGNRSSGQGHWEDAEESEPAGTVSPAPLFSTNTYERLALLFGSLGLLGVGNNLLVLVLYYKFQRLRTPTHLFLVNLSLSDLLVSLFGVTFTLVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINYSWAWRAITYIWLYSLAWAGAPLLGWNRYMLDIHGLGCTVDWKSKNANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFFMIFTFLICWMPYIVIRFLVVNGYGRLVTPTISIVSYLFCKSSTVYNPVIYIFMIRK 0

>ENCEPH_canFam Canis familiaris (dog) XP_854433 full
0 MMRRVKLTLIPAAVLDIESQAPKDESLYFSICHFCPQKGFLEFQRLRTPTHLLLVNLSLSDLLVSLFGVTFTFVSCLRNGWVWDSVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDVHGLGCTVDWKSKDANDSFFVLFLFLGCLVVPMGVIVHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFLMIFIFLIFWMPYIVICFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIIMIRK 0
0 FRRSLLQLLCFRPLRCQRPAKDLPANGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESVSIDDSDKTSVSKVDVIQVRPL* 0

>ENCEPH_felCat Felis catus full
0 MYSRNRSGGQGHWEGGGAAGAERQGPAGTLSPAPLFSPGTYERLAMLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GTVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDVHGLGCSVDWKSKDANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFLMISTFLIFWMPYIVICFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPTNGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDSDKTSVSKVDVIQVRPL* 0

>ENCEPH_bosTau pseudo frag
0 P-----SASG---RRGG----A-----G*SSLTLPVSEGAYERVV-LLGSVGLPGVGSNLLVLVIYLKLPRLRSPARLLLLHVSLGDLLPSVLQAALAFAFPLRGSRVGGTTIGEWDGFSSSL* 1
2 GIVSIITLTRLAYECYICVIHARVINFPQAWRTIPCIWLSSTVWSGASLLGWNNHILDMHGPGCTGDWPSKDTSHSSFVLFLFLGCL    GVIAHCHGHILFSIQ 
0 F*RALLQLLCF*LLRCQIPAKDLSAVGREMRLTSSVKSQKDRDVTERQG-QAKEKRTFNSSSIIFIITNDESLSVGDSDRTNGSKVDVIQVHPL

>ENCEPH_turTru Tursiops truncatus pseudo frag
0 NCGGGGAGWEGG-----EGLWPGQPSLTQPV-SQGAYELLVLLLGSVGLLGVGSSLLVLVLYLKFPRLRSPSRLFLLHVGLGNLLPSVLRAALAFAFRPRGGVVGGATNCVWDGFSNSLW 1
2 GIFSIITLTTLACERYIGMIHNRVISFSWAWRAITYIWLYSLVRSGSPLLG*HRYILDVHVLGCAVDWKSKDTSDSSFVLFLFLDCMVVPVGVIAHCYGHILYSIRK 0
0 FRRALLQLLCFRLQRCQ*PAKDLPAVGSEMQIQLIVMPQKDRDRPKKKLTFNSSSIIFVITNDESLSVD-GERTSGS*VDVIQVCPL* 0

>ENCEPH_susScro no coverage

>ENCEPH_vicVic pseudo pseudo frag
2 GIVSIISLTVLAYECYIHVVHARMITFSWTWRAVTYIWLYTLVWSGVPLMG*NRYIL-FHGLGCAVDWKSKDANDFCFVLFLFLGSLVVPVGVIAHCYGHILYSIEL 0
0 RGVEDLQTIKVIRILRYENKLARMCFCMTFTFMILWMPYVVICFLMFSDGGHLVTLTVFIVS*PFTNSSTVYDAAFYIFMIRK 0
0 FQRALLHLLCFRLLRYQQPAKDLPTYQS*MQIRPIEMSQKVRDRPKKKVIFNSSPIIFIITHDGSLSVDDKD

>ENCEPH_myoLuc Myotis lucifugus weak frag
0 MFSGNRNG--GQFRGGQLGLGHRGVGASGTLGPRAFLKNIYFYSFERRR

>ENCEPH_pteVam Pteropus vampyrus 86%=homSap full
0 MHSGNRSGGLDSWEGGGAAGAEGPGLAGTLSPGSVFNPSTYERLALLLGSIGLLGVANNLLVLVFYYKFQQVRTPFYLFLVNISFSDLLVSFFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GTVSMTTLTVLAYERYIRVVQARAIDFSWAWRTITYIWLYSLGWSGAPLLGWNRYILDVHGLGCAVDWKSKDANDSSFVLFLFLGCLVVPVVVIAHCYGHILYSVQM 0
0 LRCVEDLQTIQVIKILRYEKKMAKMCFLMIFTFLISWMPYIVICFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRK 0
0 FRRFVLQLLCFRPLRCRRPATDLPAGGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFVITSDESLSVDDSDKINGSKADGIQVRPL* 0

>ENCEPH_equCab Equus caballus full
0 MTAGTRAGGQGSWEGGGAAGAEGPGPAGPLSPAPLFSPGTYERLALLLGCLGLLGVGNNLLVLVLYSKFPRLRTPTHLLLVNISLSDLLVALFGVTFTFVSCLRNGWVWDAVGCAWDGFSSSLC 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRALTYIWLYSLAWSGAPLLGWNRYILDIHGLGCAVDWKSKDANDSTFVLFLFLGCLVVPMGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVMKILRYEKKLAKMCFFMIFTFLIFWMPYIVICFLVANGYGHLVTPTVSIVSYLFAKSSTIYNPIIYIFTIRK 0
0 FRRSLSQLLCFRLLRCQRPAKDQPPVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVHDSDKINGSKVEVIQVRPL* 0

>ENCEPH_eriEur no coverage

>ENCEPH_sorAra pseudo frag
0 RSVHTSRRGLDAGDRGGAPGATEPGRADDAVLSAALLLGAGRGTLLVLILHQKCRRPLTSPLAQLGPVNVSRGKLLVSLFGITFVFFLRNCWVWETEGRGAFSCSVL
                              

>ENCEPH_loxAfr Loxodonta africana 2 exons in browser, 1 2x full
0 MYSGNRSGGQDLWEGGGGSGGAGPAGTLSPAPVFRSGTYERLALLVGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLFLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIASITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDTHGLACTVDWKSNNSSDSSFVLFLFLGCLVVPVGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILRHEKKLAKMCLFMIFTFLICWMPYIVICFLVVNGYGHLVTPTISIVSYLFAKSSTVYNPVIYTFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPVVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVNNIDKTNGSKADVIQIRPL* 0

>ENCEPH_echTel Echinops telfairi no coverage

>ENCEPH_proCap Procavia capensis ok frag
2 GIASITSLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDTHGLACTVDWKSNNTNDSSFVLFLFLGCLVVPVGVIVHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCLFMILTFLICWMPYIVICFLMVNDYGYLVTPTISIVSYLIAKSSTVYNPVIYTFMIRKV 0
0 FRRSLFQLLCFRLLRCQRPAKNKPEVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVNDTDKINGSKADVIQVRPL* 0

>ENCEPH_dasNov Dasypus novemcinctus  pseudo
0 MYSGNRSSGHES---GGPT--------GTLGSAAFFSPRTYERLALLAGAGGLLGAGGHLLVLALRCALPQLRSPPRRLLVTASLGDPLVSVFGVAFTCAACLRSG-VWDPAGCVGDGFGSGLC 1
2 GIVSTSSLTGLASEHSIRVVHASLISFSWAWAWLYSLAWSGVPLLGWDRYVLDVHRRGCTLNLRARDSSASSRVLFLFLGCVAVPVGVTVHCHGHILHSIRM 0
0 FLCVEGLQTVQVIKILKYEKKAATMCLVVVASFLMGWMPYIAIHFSVVNGYEHLVTPVVSTVSRLFAKSSPVYNPVIYIIMIRK 0
0 FHRSFL*LLFLQLLRCQRPAQDLPVVESEMQVRPTVMSQKDRHRPKKKVTFNSSSIIFIITSDESVSVNGSDKTNGSKFDVI     * 0
                                                                                                                                                                                                                                                                       
>ENCEPH_choHof Chololepis hoffmanni so-so frag
0 MYSGNRSGGRDYWEGGGGAGAEGPGPTGTLSPALVFSPGTYERLAGLIGSIGLLGAGNNVLVLILYYKFQRLRTPTHLFLVNISFSDLLVSLFGVTFTFISCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVVNFSWTWRAITYIWLYSLACSGASLLGWNRYTLDIHGLACSVNWKSPDSSDSSFVLFLLLDCLTGPVAVIAHCY 
0 LRCVEDLQTVQVIKILRYEKKVAKMCFVMIATFLMCWMPYIVICFLVVNGYGHLVTPTVSIVSHLFVKSSTVYNLVIYIFMLRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPVVGCEMQIRPIVMSQKEGHRPKKKVTFNSSSIIFIITSDESISVDGSDKTNGPKVDVIQVRPL* 0

>ENCEPH_monDom Monodelphis domestica (opossum) encephalopsin OPN3 75%=homSap full
0 MYSDNSSDDGGGGYWGSGRAGGASGTGVTGEPGPEGSPRQAPLFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 1
2 GIVSIMTLTVLAYERYNRIVHAKVINFSWAWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVIFLFFGCLMLPVGVMAYCYGHILYAIRM
0 LRCVEELQTIQVIKILRYEKKVAKMCFLMIAIFLFCWMPYAVICLLVANGYGSLVTPTVAIIASLFAKSSTAYNPIIYIFMSRK 0
0 FRRCLLQLLCFRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDENDKNSGTKVNVIQVRPL* 0

>ENCEPH_macEug Macropus eugenii ok 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

>ENCEPH_taeGut Taeniopygia guttata mrna CK301424 70%=homSap full
0 MPAGNGTGTSGRPAPAAPEQEVPGERPLFSAGTYELLALLVATIGMLGLCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVFGVSLTFMSCLRSRWVWDAAGCVWDGFSSSLF 1
2 GIVSIMTLTALAYERYIRVVHAKVIDFSWSWRAITYIWLYSLAWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDTSFVLLFFLGCLVAPVGIMAYCYGHILHAVRM 0
0 LRCVEDFQTVQVIKLLRYEKKVAKMCFLMISTFLICWMPYAVVSLLITYGYSNLVTPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRRCLLQLLCFRLMRFQRTMRETPATGSDKPIRPIVLSQKAGDRPKKKVTFSSSSVIFIITSDDAEQIEDSSKHNETKVNAIQVKPL* 0

>ENCEPH_anoCar Anolis carolinensis (lizard) 70%=homSap OPN3 full
0 MFSANGTRSGAGSDLEPGPGQQQQQREASEEEERGAGLSPFSAGTYELLALLVAAIGLLGLCNNLLVLVLYAKFKRLRTPTHLFLVNISLSDLLVSLFGVSFTFGSCLRHRWVWDAAGCVWDGFSNSLF 1
2 GIVSIMTLTVLAYERYIRVVHARVIDFSWSWRAITYIWLYSLAWTGAPLLGWNHYTLEIHGLGCSVDWQSKEPSDSSFVLFFFLGCLAAPVGIMAYCYGHILHAIRM 0
0 LRCVEDLQSIQVIKILRYEKKVAKMCFLMVTTFLICWMPYAVVSLLIAYGYGHLITPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRRCLVQLFCVQFLRFKRTLKEQPAIESNKPIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDDTEQIDVSTKCSDTKINVIQVKPL* 0

>ENCEPH_xenTro Xenopus tropicalis (frog) 45%=homSap full 
0 MPVTNGSHNNSISWLHSKDMFTEDTYHFLALIVATVGFLGLVNNLLVLILYCKFKRLQTPTNLLFFNTSLCHFVFSLLAITFTFMSCVRGSWAFSVEMCVFHGFSKNLL 1
2 GIVSFGTLTVVAYERYARVVYGKYVNSSWSKRSITFVWVYSLAWTGFPLIGWNLYTFETHKLDCSFEWTATDPKDTAFVLLFFLACITLPLSIMAYCYGYILYEIQK 0
0 LRSVKNIQNFQEITILDYEIKMAKMCLLMMLTFLIGWMPYTILSLLVTSGYSKFITPTITVMPSLLAIASAAYNPVIHIFTIKK 0
0 FRQCLVQLLPPINFHPPINPPINNFWRLLKNLNGRLAMKKVKPVLGKGRSHNRPEKKVPPINFSSSDFFTRTTSDTGTHGITESTKGKRTNVRLIQVHPL* 0

>ENCEPH_danRer Danio rerio (zebrafish) NM_001111164 mrna 61%=homSap full
0 MNSFNETPTEAHLENYNYIFADETYKLLTFTIGSIGVLGFCNNIIVIILYSRYKRLRTPTNLLIVNISVSDLLVSLTGVNFTFVSCVKRRWVFNSATCVWDGFSNSLF 1
2 GIVSIMTLSGLAYERYIRVVHAKVVDFPWAWRAITHIWLYSLAWTGAPLLGWNRYTLEVHQLGCSLDWASKDPNDASFILFFLLGCFFVPVGVMVYCYGNILYTVKM 0
0 LRSIQDLQTVQTIKILRYEKKVAVMFLMMISCFLVCWTPYAVVSMLEAFGKKSVVSPTVAIIPSLFAKSSTAYNPVIYAFMSRK 0
0 FRRCMLQMLCSRLTSLQHTIKDRPLSRIEHPIRPIVMSQSRTDRPKKRVTFSSSSIVFIIASHDTHPLDITSKCNDEPDINVIQVRPL* 0

>ENCEPH_takRub Takifugu rubripes (pufferfish) homSap=61% full
0 MNPANGSRSERSAEQLLFSGDTYRVLAFTIGTIGAFGFCNNFVVLALYCRFKRLRTPTNLLLVNISLSDLLVSLFGINFTFAACVQGRWTWTQATCVWDGFSNSLF 1
2 GIVSIMTLAALAYERYIRVVHAQVVDFPWAWRAIGHIWLYALAWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVQM 0
0 IRSIQDLQTVQIIKILRYEKKVSVMFFLMISCFLLCWTPYAVVSMMVAFGRRSMVSPTMAIIPSFFAKSSTAYNPLIYVFMSRK 0
0 FRHCLLQLLCSRLSWLQRSLKERPLAPVQRPIRPIVMSRPCGKGNRPKKKVTFSSSSIVFIITSDDFGQLDVTSKSGDSADVNAIQVRPL* 0

>ENCEPH_gasAcu Gasterosteus aculeatus (stickleback) 58%=homSap full
0 MNPDNGTREERSTDHSIFAVGTYKLLAFAIGTIGVFGFCNNVVVIVLYCKFKRLRTPTNLLVVNISLSDLLVSVIGINFTFVSCIRGGWTWSRATCIWDGFSNSLF 1
2 GIVSIMTLASLAYERYIRVVHAQVVDFPWAWRAIGHIWLYSLVWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVQM 0
0 LRSIQDLQTVQIIKILRYEKKVAVMFLLMISCFLLCWTPYAVVSMMEAFGRKNMVSPTVAIIPSFFAKSSTAYNPLICVFMSRK 0
0 FRRCLMQLLCSRVTCLQCNLKERPLAPVQRPIRPIVVSAACGGGRVRPKKRVTFSSSSIVFIITRNDIRHTDVTSNTRESSEANVFQVRPL* 0

>ENCEPH_oryLat Oryzias latipes  58%=homSap full
0 MNPANESRAGRHEERSVFAVGTYKLLTVIIGTIGVFGFCNNLLVILLYCKFKRLRTPTSLLLVNISLSDLLVSVVGINFTLASCVKGRWMWSQATCVWDGFSNSLF 1
2 GIVSIMTLAALAYERYIRVVHAQVVDFPWAWRAIGHIWLYSLAWTGAPLLGWNRYTLEIHQLGCSLDWASKDPNDAAFILLFLLGCFFVPVGIMIYCYGNILYAVRM 0
0 LRSIEDLQTVQIIKILRYEKKVAAMFLLMISCFLVCWTPYAVVSMMEAFGKKSMVSPTVAIVPSFFAKSSTAYNPLIYVFMNRK 0
0 FRRCFLQLLGSRLCSKISWLQCTLKEHPLTPVERPIRPIVASTSCGSRHRPKKRVTFNSSSIVFMITGDEFQQLDVTSKSRNSSEANVFHVRPL* 0

>ENCEPH_calMil Callorhinchus milii (elephantfish) wgs frag  
0 MNPTNSTEPQEEHLFSPNTYKLLAVIIGTIGIVGFCNNILVLLLYYKFKRLRTPTNLLLVNISVSDLLVSVFGLSFTFVSCTQGRWGWDSAACVWDGSHSLF 1
2 GTVSIVTLTVLAYERYIRVVNAKATNFPWAWRAITYTWFYSLAWSGAPLV
0 0
0 YRRCLSQLFCSHLMSLQWSIKDPSSKARNDMPVKPIVLSQKGDRPKKRVTFSSSSIVFIITSDDTQELGSIAGSNATQISIVQVQPL* 0

>ENCEPH_squAca Squalus acanthias (dogfish) Gt 0...2...0.0 indel x x x x 202 aa 000 nm no_ref genome fragment   
0 MNAANSTDTREESLFSPGTYQVLAVIIGTIGVVGFCNNLLMLVLYCKFKRLRTPTNLFLVNISISDLLLSVFGVIFTFVSCVKGRWVWDSAACVWDGFSNCLF 1
2 GISSIMSLTVLAYERYIRVVNATAIDFSWAWRAITYIWLYSLAWTGAPLIGWNSYTLELHRLGCSVNWDSRNPSDTSFVLFLFLGCLLCPIGVIAYCYG

>ENCEPH_petMar Petromyzon marinus (lamprey) no_ref genome fragment   
0 MQSPKQDSLHYAGDTGAKAAPDSAQGNASALGSNFLLHGGDLGEGSTAFSAATFRLLAGVVGTIGVAGFLNNLLLVALFVGFKRLQTPTNLLLVNISLSDLLVSVFGNTLTLVSCVRRRWVWGNGGCVWDGFSNSLF 1
2 GIVSISTLTALSYERYARLIKAQVLDFSWAWRAVTYTWLYSAAWTGAPLLGWSRYVLEKHGLGCSIDWASSNPPDAAFVLFFFLGCLAAPLLVMGFCFGRIALAITQ 0
0 CWSPYAVASLFVASGFEHLVSPPVSIVPSLLAKSNAVCNPLLFLLMSGN 0

>ENCEPH4_braFlo Branchiostoma floridae (amphioxus) 12435605 AB050608 encephalopsin Amphiop4 new exon 12 and 34 + perfect fit   
0 MALYNNTSSPSQDLLWDAPYSQGHIWDNSSASNSSEDVMDQGKVELQDFSDAGYTAIATCLALI 1
2 GFVGFTNNFVVILLIGCHRQLRTPFNLLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANSLF 1
2 GIVSLVTLSALAFERYCVVVRSSDMLTYKSSLVVITFIWLYSLLWTSLPLLGWSSYQFEGHN 0
0 VGCSVNWVQHNPDNVSYIVTLMVTCFFVPMVVVCWSYAWIWRTVRM 0
0 SSEAKPECGNSQNAGRLVTTMVVVMIICFLVCWTPYAVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ 0
0 FREFLLARLQRVCCRQQAVPRVTPMDDNVHVRLGGEGPSQSQQFLPAGENVENVDMLEYVQENCKPKADSLSTISE* 0

>ENCEPH4_braBel Branchiostoma belcheri (amphioxus) no_ref genome encephalopsin Amphiop4 introns from braFlo   
0 MPLYNTSSGPTQGLPWDTPYSQDPIWNDSSPSNSSEDAVVDQGRGELQDFSDAGYTAIATGLALI 1
2 GLVGSMNNFVVILLIGCHRQLRTPFNLLLLNVSVADLLVSVCGNTLSFASAVQHRWLWGRPGCVWYGFANSLF 1
2 GIVSLVTLSALAFERYCVVVRSSEMLTYKSSLGMIAFIWMYSLLWTSLPLLGWSSYQFEGHS 0
0 VGCSVNWVKHNVNNVSYIITLMVTCFFVPMVVVCWSYACIWRTVRM 0
0 SAEMKSEFGNPQNTGRLVTTMVVVMIVCFLVCWTPYTVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ 0
0 FREFLLARLRTFCCRQPRMLRVTPMDDNAHARLVGEGPSHAQQVIPSEENGENVEMRKVQGNQLKADSLSTISE* 0

>ENCEPH6_braFlo browser duplicated frag
0      VAAILALIGVLGIVNNSTTLYLVGRYKQLRTPFNILMVNLSVSDLLMCVLGTPFSFVSSLHGRWMFGHSGCEWYGFICNF 1
2 GIVSLITLTVISYERYLLMKRLPNERILSYRAVALAVVFIWCYSLLWTAPPLVGWSSYGPEGYGISCSVNWESRTANDTSYIVAYFVGCLVFPVAIIVISYTRLLILYMRQ 0
0 APSAPMQMLVRREKRVTKMVVVMIMGFTICWTPYTIVALIVTCGGEGIITPAAATVPALFAKSSVVYNAAIYVAMNNQ 0
0 FRKCFLRSLNCRSQPRDPSSQQYTLKTNQVGMSTSGSQAARTADRIKTVHVATANPQDHRSSSGQAVEDNGGFRKSLTHSLPLNSISTLLEAEK* 0

>ENCEPH_strPur Stronglyocentrotus purpuratus GLEAN3_03451 modified terminal exon by extending penultimate to stop codon
0 MSLATKKHFIRNAVEEGGHLLEKWDKGG 2
1 YAFIMTFLGLNSLMSHAVIAVDRYLVITKPHF 1
2 GIVVTYPKAFLMISIPWVFSFAWAVFPLAGWGEFTYEGTGAWCSVRWDSDQPQIMSYVLAMMFLTFISSIVIMMYCYICIFLTTRRMPRWATSNSIKTHERNRRRR 2
1 EQKLLKTLIAIAIAFLVAWSPYAITSMIVVFGGSELLSLTATTLPSLFAKSSVMINPIIYAVTSRVFRKSLKK 0
0 MLTSFFPGCMTYIMTDKSPPSSSRPIQLGLCKYHFLY* 0

Reference set of 17 TMT encephalopsins from elephantshark to marsupial

>TMT_monDom Monodelphis domestica TMT opsin XM_001372110 MSR full
0 MSNNLTTNLSLEALLSASEDKQRNGLSRTGHTIVAVFLGIILIFGSISNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLSGTTLSFASSIQGRWIGGKHGCRWYGFANSCF 1
2 GIVSLISLAILSYERYRTLTLCPGQGADYQKALLAVAGSWLYSLVWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILVMVYFYGRLLYAVKQ 0
0 VGKIRKTAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYVLMNKQ 0
0 IKGEKTLDRAAGLKVKKTRELGDHMLRVSRSVQITD* 0

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

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

>TMT_galGal Gallus gallus XM_001234388 mRNA multiple tissue opsin full
0 MNHTWTYNLSFGAPTDPVEPRAGLSRNGHTVVAVFLGFILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNISISDMLVCISGTTLSFASNIHGKWIGGEHGCRWYGFVNSCF 1
2 GIVSLISLAVLSYERYSTLTLCNKRSDDYRKALLAVGGSWVYSLLWTVPPLLGWSSYGIEGAGTSCSVRWSSETAESTSYIICLFIFCLVIPVMVMMYCYGRLLYAVKQ 0
0 VGKIHKNTARKREYHVLFMVITTVICYLVCWIPYGVIALLATFGKPGVVTPVASIIPSILAKSSTVCNPIIYILMNKQ 0
0 FLTLKLNEGRSGSFENVFCSKKFEKYALLMLSY* 0

>TMT_taeGut Taeniopygia guttata last exon questionable full
0 MNHTWMYNLSFGAPAHPVEPRAGLSRSGHTVVAVFLGLILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNISVSDMLVCISGTTLSFASNIRGKWIGGDHACRWYGFVNSCF 1
2 GVVSLISLAVLSYERYNTLTLCHKRSDDFRKALLAVAGSWIYSLVWTVPPLLGWSSYGVEGAGTSCSVRWSSESAESTSYIICLFVFCLVVPVMVMMYCYGRLLYAVKQ 0
0 VGKIHKNAARKREYHVLFMVIPTVICYLVCWIPYGVIALLATFGKPGAVTPITSIIPSILAKSSTVCNPIIYILMNKQ 0
0 ILTLKFDNGRSGNFESVFCGRKSAKYA* 0

>TMT_anoCar full
0 MSELSSNLTFNMSTSIEEPGSGLSRMGHNIVAVFLGLILVFGFLNNLVVLILFCKFKTLRNPVNMLLLNISASDMLVCISGTTLSFVSNIYGRWIGGEHGCRWYGFVNSCF 1
2 GIVSLISLAILSYERYSTLTQTNKRGSDYQKALLGVGGSWLYSLIWTVPPLIGWSSYGLEGAGTSCSVRWTSETLESVTYIICLFIFCLAIPVLVMIYCYARLFYAVKQ 0
0 VGKLRKTSARKREFHVLFMIITTIICYLICWMPYGVIALLATFGRPGLVSPVASVIPSILAKSSTVFNPIIYILMNKQ 0
0 FQFYKCFLMLLHCQPSSVADGETICQSKVMAIHQNQKAQGGVILKSQVVPQMDEKAICLLSPESSLDPVLESTPQLSKENSFL* 0

>TMT_xenTro full
0 MSTIKNWTTNISVENSMSYIENDLSLPTEAVLSRTGHTVVAIFLGFILIFGFLNNFVVLILFCKFKTLRTPVNMMLLNISASDMLVCVSGTTLSFTSSIKGKWIGGEYGCQWYGFVNSCF 1
2 GIVSLISLAILSYERYSTLTLYNKGGPNFKKALLAVASSWLYSLVWTVPPLLGWSSYGREGAGTSCSVRWTSESVESVSYIICLFIFCLALPVFVMLYCYGRLLYAVKQ 0
0 VGKIRKIAARKREYHVLFMVITTVICYLLCWLPYGVVALLATFGRPGVISPVASVVPSILAKSSTVFNPIIYILMNKQ 0
0 FYKCFLILFHCHPTSSADGKSICQSNYTVIQLNQKLNNIVAIPGQTQIPESVDKMPCIHRQNNESPSDQMPQSTTEHLISGT* 0

>TMT_danRer Danio rerio NM_001118899 full
0 MIVSNLSVLSCRRNSALCLGAVEGHLEASSSYRTLSPTGHILVAVSLGFIGTFGFLNNLLVLVLFGRYKVLRSPINFLLVNICLSDLLVCVLGTPFSFAASTQGRWLIGDTGCVWYGFANSLL 1
2 GIVSLISLAVLSYERYCTMMGSTEADATNYKKVIGGVLMSWIYSLIWTLPPLFGWSRYGPEGPGTTCSVDWTTKTANNISYIICLFIFCLIVPFLVIIFCYGKLLHAIKQV 0
0 SSVNTSVSRKREHRVLLMVITMVVFYLLCWLPYGIMALLATFGAPGLVTAEASIVPSILAKSSTVINPVIYIFMNKQ 0
0 FYRCFRALLNCDKPQRGSSLKSSSKTKPFRPGRRTDNFTFMVASVGPNQTNPVEDGPPSADNTKPAVLSLVAHYNG* 0

>TMTa_takRub Takifugu rubripes (pufferfish) -CALD1 +TNK2 -RAB18 +ABI1 12670711 AF402774 encephalopsin-related TMT multiple tissue full
0 MIVSNVSLSGCAGVNGAVCAAEGHQAGGSDRSTLTPTGNLVVSVFLGFIGTFGLVNNLLVLVLFCRYKMLRSPINLLLMNISISDLLVCVLGTPFSFAASTQGRWLIGEAGCVWYGFANSLF 1
2 GVVSLISLAVLSFERYSTMMTPTEADPSNYCKVCLGITLSWVYSLVWTVPPLFGWSSYGPEGPGTTCSVNWTAKTTNSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQ 0
0 VSGINASTSRKREQRVLCMVVIMVICYLLCWLPYGVVALLATFGPPDLVTPEASIIPSVLAKSSTVINPIIYVFMNKQ 0
0 FYRCFLALLCCQDPRSGSSMKSSSKVATKAKGVTPTGQRRTDFLYMVASLGRPAATIPQLGPSFDATNDFTKPPSSDTIKPVVVSLAAHCDG*

>TMTb_takRub Takifugu rubripes (pufferfish) +TFRC +CHES1 -MYEOV2 -ARHGAP21 encephalopsin-related  
0 MIVCNVSLSCAHCPGEGTAANDAYAQASGSLATPTLSQRGHLVVAVCLGFIGTVGFLSNFLVLALFCRYRALRTPMNLMLVSISASDLLVSVLGTPFSFAASTQGRWLIGRAGCVWYGFVNACL 1
2 GIVSLISLAVLSYERYCTMVSSTIASNRDYRPVLGGICFSWFYSLAWTVPPLLGWSRYGPEGPGTTCSVDWRTQTPNNISYIVCLFTFCLLLPFFVILYSYGKLLHTIRQ 0 
0 VRRVSSTVTRRREHRVLVMVVAMVVCYLICWLPYGVTALLATFGPPNLLTPEATITPSLLAKFSTVINPFIYIFMNKQ 0
0 FYRCFRAFLNCSTPKRDSTVRTFTRISLRALRQDQQQKGSALAPSSARPTPNSIHESSLKGSHSTPSNGGAAAAKSPAANRSKPKLILVAHYRE* 0

>TMT_tetNig Tetraodon nigroviridis full
0 MIASNASVSGCAGVHGAACAADAPPAGGSHRSSSSLTPTGNLVVSVFLGLIGTSGLVSNLLVLVLFCRFKVLRSPINLLLVNISVSDLLVCVLGTPFSFAASTQGRWLIGAAGCVWYGFVNSLFG 1
2 GIVSLISLAVLSFERYSTMMTPTEADSSNYCKVCLGIGLSWVYSLLWTVPPLLGWSSYGPEGPGTTCSVNWTAKTANSVSYIICLFVFCLILPFLVIVFCYGKLLCAIRQ 0
0 VSGVNASMSRRREQRVLFMVVVMVICYLLCWLPYGVVALLATFGPPGLVTPAASIIPSILAKSSTVINPVIYVFMNKQ 0
0 FSRCFLSLLCCEDPRSSTSLRSSSRVTTKAVRGGTLTGQRRTNHLLYMVAALGRPVATAMPQLGPSFDATYDITKAPSSDNHQPVVVSLEAHG* 0

>TMT_gasAcu  Gasterosteus aculeatus (stickleback) genome +TNK2 +ENC full
0 MIVSNLSLSGCAGVSSALCAAAGEGHLSGGSHRNTLTPTGHLVVAVCLGFIGTLGLMNNLLVLVLFCRYKMLRSPINLLLINISISDLLVCVLGTPFSFAASTQGRWLIGEGGCVWYGFANSLFG 1
2 GIVSLISLAVLSYERYSTMVAPTEADSSNYHKISLGITLSWVYSLIWTAPPLFGWSHYGPEGPGTTCSVDWTARTANSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQV 0
0 VSGINASLSRKREQRVLFMVVIMVVCYLLCWLPYGIMALMATFGPPGLITPVASIIPSVLAKTSTVINPVIYVFMNKQ 0
0 FYRCFKALLRCEAPRPSSSLKSSSKVPTKAMRGAAVTGPRHTNNFLFVVASLGRPVATIPQLGPSVEPTIDVTGGPSSDNNKPVIVSLVAQCDG* 0

>TMT_oryLat Oryzias latipes (medaka) genome SLC12A3 two frags
0 MLVSNVSLGGCAEFNSALCAGAGEEHLGGGSYRTTLTPTGHLIVAVCLGFIGTFGLVNNLLVLVLFCRYKILRSPINLLLINISISDLLVCVLGTPFSFAASTQGRWLIGEGGCVWYGFANSLCG 1
2 GIVSLISLAVLSYERYSTMMTPAEADSSNYRKISLGIILSWGYSLLWTLPPLFGWSHYGPEGPGTTCSVDWTAKTANNISYIICLFVFCLIVPFMVIVFCYGKLLYAIKQV 0
0 VSGINVSVSRKREQRVLFMVVIMVICYLLCWLPYGIMALLATFGPPDLVTPEASIIPSVLAKTSTAINPVIYVFMNKQ 0
0 * 0

>TMT_pimPro Pimephales promelas frag
   GHLVVAVCLGFIGTGFLNNTLVLILFCRYKVLRSPMNYLLVSIAVSDLLVCVLGTPFSFAASTQGRWLIGRAGCVWYGFINSCL 1
2 GVVSLISLAVLSYERYCTMMGATQADSTNYKKVAMGIAFSWIYSMVWTLPPLFGWSCYGPEGPGTTCSVNWAARTANNVSYIICLFFFCLILPFIVIVYSYGRLLQAITQ 0
0 VSRINTVVSRKREQRVLFMVITMVVCYLLCWLPYGIMALLAAFGRPGLVTPAASIVPSVLAKTSTVINPIIYIFMNKQ 0
0 FCRCFHALIMCTTPQRGSSFKNSSKVTKTLRTVRRANGQNVTFAVASAGHPTICAPH

>TMT_calMil Callorhinchus milii (elephantfish) wgs frag 
0 MLNSSPNSSPSLPLSQVGWTGLSRTGLTVVAVCLGIIMVLGFLNNLLVLVLFCKYKVLRSPMNMLLLNISVSDMLVCICGTPFSFAASVQGRWLVGEQGCKWYGFANSLF 1
2 GIVSLMSLTILSYDRYITITGTTEADITNYNKTIVGIALSWIYSLMWTLPPLFGWSNYGPEGPGTTCSVNWQSKEVSSKSYIICLFIFCLLMPFLVIVYCYGKLVLAVRK 0
0      AQTREHRILLMVISMVTFYLLCWLPYGTVALIGTFGNADLITPTCSVIPSILAKSSTVINPVIYVIMNKQ 0

>TMT5_braFlo Branchiostoma floridae (amphioxus) no_ref genome encephalopsin extra 0 intron   
0 MLGMHNVMNATDYDNNNATFAAWNFQRNGTTEEEVEFSGFDTVAVVIAAIGIAGFLSNGAVVLLFLKFRQLRTPFNMLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 1
2 GLVSLISLAVISYERYRMVVKPKGPGSSYLTYNKVGLAIIFIYLYCLLWTTLPIVGWSSYQLE 0
0 GPKISCSVAWEEHSLSNTSYIVAIFIMCLLLPLLIIIYSYCRLWYKVKK 0
0 GSQNLPPAIRKSSQKEQKIARMVVVMITCFLVCWLPYGAMALVVSFGGESLISPTAAVVPSLLAKSSTCYNPLVYFAMNNQ 0
0 FRRYFQDLLCCGRRLFDASASVNTCNTSAMPRHSPVFQKPDSDQYNGIQKSREPQMRTTGQNAPYRQWIEMQTIAVVVKADEVNNKFGEVKT* 0

>TMT5_braBel Branchiostoma belcheri (amphioxus)  AB050609 encephalopsin Amphiop5 extra Nfrag in mrna   
0 MLGIYNVVNATEYGNNTTFAAWDFKRNGTGGEEEVEFFGYDAVAGVIAIIGVVGFVSNGAVVVLFLKFPQLRTPFNLLLLNMAVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 1
2 GLVSLISLAVISFLRYRMVVKPKGPGSSYLTYTKVGLAILFIYLYCLLWTTLPIAGWSSYQLE 0
0 GPKIGCSVAWEEHSWSNTSYIVVLFITCLFAPLLIIVYSYYRLWHKVKQ 0
0 GSRNLPAAMRKSSQKEQKIAMMVIVMITCFMVCWLPYGAMALVVTFGGERLISHTAAVVPSLLAKSSTCYNPVVYFAMNSQ 0
0 FRRYFQDLLCCGRRLFDVSQSVVTGNTAMPRNNSQGFRKDDSDQKQDNGLPKQSEGPMCDHSSNESQMEGSRHNTAASQQWIEMQTIAVVVKAVEVDTSAANEP* 0