Cryptochrome evolution

Introduction to Cryptochromes

Cryptochromes are large flavoproteins with a curiously complex evolutionary history, beginning billions of years ago as repair enzymes for dna damaged by ultraviolet light. An old gene duplication followed by specializing divergence gave rise to two paralogs repairing distinct types of dna damage (cyclobutane pyrimidine dimers and 6-4 pyrimidine-pyrimidone pairs). These photolyases initially used FAD activated by visible blue light to undo the damage done by UV.

Since FAD has relatively low adsorbance, photolyases evolved a second site for an antenna chromophore with better light harvesting capabilities that could transfer its excitation to the FAD at the active site. This elusive second molecule may be FMN, folate, or a deazaflavin called Fo (once thought restrict to methanogenic archaea). In the case of the much-studied Drosophila, both the photolyases utilize Fo, making it a new vitamin for this species since the Fo biosynthetic genes are absent.

A second round of gene duplication of the 6-4 photolyase gave rise to a cryptochrome which retained the conformational change induced by FAD binding of blue light but lost dna repair capacity, instead specializing in entraining the day/night circadian rhythm cycle. A third round of gene duplication gave rise to two cryptochromes CRY1 and CRY2.

These four genes were retained in various combinations in different clades during the subsequent course of evolution, causing endless comparative genomic confusion. For example, Drosophila did not retain CRY2 unlike other insects and placental mammals lost both photolyases though marsupials retained one. Rayfinned fish had a series of further duplications within the gene family. Over all this, the fold, exon structure and FAD binding site were largely conserved, while antenna molecules and dna repair capacity were sometimes lost, even as altogether new binding properties developed giving some family members important new regulatory capacities.

(to be continued shortly)

Vertebrate CRY1 reference sequences

>CRY1_homSap Homo sapiens (human)
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSAENIPGCSSSG 1
2 SCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSMGTGLSGGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_panTro Pan troglodytes (chimpanzee) XM_509339
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSAENIPGCSSSG 1
2 SCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSVGTGLSGGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_ponAbe Pongo abelii (Sumatran orangutan) XM_002823690
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDASLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSAENVPGCSSSG 1
2 SCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSMGTGLSGGKRASQEEDTQSIGPKVQRQSTN* 0

>CRY1_nomLeu Nomascus leucogenys (gibbon) XM_003269977
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSAENIPGCSSSG 1
2 SCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSMGTGLSGGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_macMul Macaca mulatta (rhesus) NM_001194159
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGINYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSTENIPGCSSSGS 1
2 CSQGSGILHYTHGDSQQTHLLKQ 1
2 GRSSMGTGLSGGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_calJac Callithrix jacchus (marmoset) XM_002752946
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSAENIPGCTSSG 1
2 SCSQGSGILHCAHGDSQQTHLLKQ 1
2 GRSSMSTGISGGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_saiBol Saimiri boliviensis (squirrel monkey) nearly identical to marmoset
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSAENIPGCTSSG 1
2 SCSQGSGILHCAHGDSQQTHLLKQ 1
2 GRSSMSTGLGGGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_tarSyr Tarsius syrichta (tarsier) ABRT010205577 unsure if exon 2 is CRY1 or CRY2
0 2
1 FLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 0
0 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMGYSPAENTPGCSSSG 1
2 SCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSVGTGLSGGKRPSQEEDPQSIGPKVQRQSTN* 0

>CRY1_micMur Microcebus murinus (mouse lemur) 
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 IIELNGGQPPLTYKRFQTLISK SEVIEKCTTPLSDD    1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKSSPPLSLYGRYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGFMEYSPAENIPGCSSSG 1
2 NCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSMGTGFSGGKRPSQEEDTQSIGSKVQRQSTN* 0

>CRY1_otoGar Otolemur garnettii (bushbaby) AAQR03016495
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITRLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 0
0 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEIIEKCTTPLFDDHDEKYGVPSLEEL 1
2 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPASFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGINYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGSFMEYSPPENIPGCSSSG 1
2 NCSQGSGILHYAPGDGQQPHLLKQ 1
2 GRSSMGTGLSGGKRPSQEEDMQSVGPKVQRQSTN* 0

>CRY1_tupBel Tupaia belangeri (treeshrew)
0 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 0
0 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKFGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRVNSNSLLASPTGL
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLSSSGSCSQGSGILHYAHGDSQQTHLLKQGRSSMGP      1
2  1
2 GCSQGSGILHYAHGDSQQTHLLKQ  1
2 GLSSGKRPSQEEDTQSIGPKVQRQSTN* 0


>CRY1_musMus Mus musculus (mouse) NM_007771 all transcripts support longer exon 10 lost splice donor
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLVSKMEPLEMPADTITSDVIGKCMTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLER 0
0 KAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNSNGNGGLMGYAPGENVPSCSSSGNGGLMGYAPGENVPSCSGG 1
2 NCSQGSGILHYAHGDSQQTHSLKQ 1
2 GRSSAGTGLSSGKRPSQEEDAQSVGPKVQRQSSN* 0

>CRY1_ratNor Rattus norvegicus (rat) NM_198750
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLVSKMEPLEMPADTITSDVIGKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYAPGENVPSGGSGGG 1
2 NCSQGSGILHYAHGDSQQTNPLKQ 1
2 GRSSMGTGLSSGKRPSQEEDAQSVGPKVQRQSSN* 0

>CRY1_criGri Cricetulus griseus (hamster) XM_003505292
0 MGVNAVHWFRKglrlhDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDSNLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLVSKMEPLEMPAETITSDVIGKCMTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLER 0
0 KAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYTTGENLPSCSGGG 1
2 SCSQGSGILHYAHGDSQQAHLLKQ 1
2 GRSSMGTSLSSGKRPSQEEETRSVDPKVQRQSSN* 0

>CRY1_spaJud Spalax judaei (blind mole rat) AJ606298
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRW 2
1 RFLLQCLEDLDANLRKLNSRLLVIRGQPADVFPRLFKEWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERR 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTGSDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYTPGENIPNCSSSG 1
2 SCSQGSGILHYAHGDSQQAHLLKQ 1
2 GSSSMGHGLSNGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_dipOrd Dipodomys ordii (kangaroo rat) ABRO01202522 ABRO01202521
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRW 2
1 RFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCSVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYAAGDNLPGSSSSG 1
2 SCSQGSGILHYAHGDSQQMHLLKQ 1
2 GRSSMGTGLSSGKRPSQEEDSQSIGPKVQRQSTN* 0

>CRY1_speTri Spermophilus tridecemlineatus (squirrel) Ictidomys
0  2
1  
0    RDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHEASLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMAyAPGENIPGCSSSG 1
2 SCTQGSSILHNAHGDSQQTHLLKQ 1
2 GRSSMGTGLSSGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_oryCun Oryctolagus cuniculus (rabbit)
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRW 2
1 RFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITRLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSDVIEKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGQTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGINYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYSPGENIPGCSSSG 1
2 SCSQGSGILHYAQGDTQQTQLLKQ 1
2 GRSSMGTGLSSGKRPSQEEDTQSIGPKVQRQSTN* 0

>CRY1_ochPri Ochotona princeps (pika)
0  2
1  0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1  1
2 GFDTDGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0  2
1  1
2  1
2 GCPQGSGILHCGHGDSQQTHLLKQ 1
2 GRGSPDTGISSGKRPSQEEDTQSIGPKVQRQSTN* 0


>CRY1_oviAri Ovis aries (sheep) NM_001129735 19341811 19150926
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIIRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVMEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRG 1
2 GLLASVPSNPNGNGGLMGYSPGENIPGCSSSA 1
2 SCTQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSTAAGLGSGKRPSQEEDTQSVGPKVQRQSTN* 0

>CRY1_bosTau Bos taurus (cattle) NM_001105415 XM_616063
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYSPGENIPGCSSNA 1
2 SCTQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSTGAGLGSGKRPSQEEDTQSIGPKVQRQSTN* 0
+
>CRY1_susScr Sus scrofa (pig) XM_003126079
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYSPGENIPGCSSSG 1
2 SCPQGSGILHYAHGESQQNHLLKQ 1
2 GRSSTGSGLSSAKRPSQEEDTQSIIGPKVQRQSTN* 0

>CRY1_ailMel Ailuropoda melanoleuca (panda) XM_002927658
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIEKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPANPNGNGGLMGYSPGENIPGCSSSG 1
2 SCSQGSGILHYAHGDSQQTHLLKQ 1
2 GRSSMGSGLSSGKRPSEEEDTQSIGPKVQRQSTN* 0


>CRY1_loxAfr Loxodonta africana (elephant) XM_003405313
0 MGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWDITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMEPLEIPVETITSEVIGKCTTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYSPGENTPGCNSSG 1
2 SCSQGSGILHYVHGDSLLKQ 1
2 GRSPTGTGVSSGKRPSQDEETQTLGPKVQRQSTN* 0

>CRY1_monDom Monodelphis domestica (opossum) XM_003341966
0 MGVNAGHWFRKRLRLPHNPALKGCIQGADTVCCVYIRDPWFGGSSNFGANEWK 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 0
0 IIELNGGQPPLTYKRFQTLISKMEPLATPVETITPEVMHKCVTPLSDEHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGSLMAYTPGENIPGCSSGG 1
2 GYSQGSGISHYSHEDSQQAYMLKQ 1
2 GRSSLGVGGGKRPRQEEETQSINPKVQRQSTN* 0

>CRY1_macEug Macropus eugenii (wallaby) assembly frameshift
0 MGVNAVHWFRKGLRLHDNPALKECIEGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPLGRNAMQLLKNWASEAGVEVIVRISHTLYDLDK 2
1  1
2 gFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGVQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGSLMGYTTGENIPTCSSSGG 1
2 GYSQGSGISHYSHEDSQQAYVLKQ 1
2 GRNSLGGGKRHRQEEETQSIGSKMQRQSVN* 0

>CRY1_sarHar Sarcophilus harrisii (tasmanian devil) nearly identical to oppossum
0 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 0
0 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGGLMGYTSGENGPACNSGG 1
2 GYSQGSGISHYSHEDSQQAYILKQ 1
2 GRSSLSGGKRPRQEEETQSVGPKVQRQSVN* 0


>CRY1_ornAna Ornithorhynchus anatinus (platypus) XM_001508563 = rubbish, genomic frameshift, continuing exon 12
0 MGVNAVHWFRKGLRLHDNPALRDCVRGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYELDK 2
1 IIELNGGQPPLTYKRFQTLISRMDPLAMPVETITAEVMGKCMTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATSNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNANGSGGLMAYSPGENIPGCSSGGG 1
2 GVQMGASESH LLQTCVLGESHLGPSGIQQQ 1
2 GYCQGSGVLYYANGESHLTQ 1
2 GRSSLTPGLSGGKRPCQEEESQSIGPKVQRQSTD* 0

>CRY1_tacAcu Tachyglossus aculeatus (echidna) SRR000649.130490 short read transcripts corrected for frameshifts, skipped penultimate exon
0  2
1  0
0  2
1    ETITAEVMGKCVTPLSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGEAEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLTPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATSNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAImtqlrqeGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNANGSGGLMAYSPGENIPGCSSGG 1
2 GAQIGASESHLLQTCVLGESHLGPSGIQQQ 1
2  1
2 GRSSLTPGLSGGKRHCQEEESQSIGPKVQRQSTD* 0


>CRY1_allMis Alligator mississippiensis (alligator) scaffold-103537
0 MGVNAVHWFRKGLRLHDNPALRECIQGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITAEVMEKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATSNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGVQKAAKCMIGINYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNPNGNGNGGLMGYSPGENVSGCSRA 1
2 GAQMGSSDGHTVSVQPCALGESHGGSNGIQQQ 1
2 GYFQASSILHFPHGDDQQSHLLQQ 1
2 GRTSLSSGISAGKRPNPEEETQSIGPKVQRQSTN* 0

>CRY1_galGal Gallus gallus (chicken) 11684328 17324421 15459395
0 MGVNAVHWFRKGLRLHDNPALRECIRGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWSIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITPEVMQKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERH 0
0 LERKAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPESVQKAAKCVIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNPNGNGNGGLMSFSPGESISGCSSAG 1
2 GAQLGTGDGQTVGVQTCALADSHTGGSGVQQQ 1
2 GYCQASSILRYAHGDNQQSHLMQP 1
2 GRASLGTGISAGKRPNPEEETQSVGPKVQRQSTN* 0

>CRY1_melGal Meleagris gallopavo (turkey) XM_003202363
0  2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWSIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITPEVMQKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERH 0
0 LERKAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPESVQKAAKCVIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNPNGNGNGGLMSFSPGESISGCSSAG 1
2 GAQLGTGDGQTVGVQSCALGDSHTGGNGVQQQ 1
2 GYCQASSILRYAHGDNQQPHLMQP 1
2 GRASLGTGISAGKRPNPEEETQSVGPKVQRQSTN* 0

>CRY1_eriRub Erithacus rubecula (robin) AY585716
0 MGVNAVHWFRKGLRLHDNPALRECIRGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITPEVMKKCTTPVFDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 ASVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPESIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNPNGNGNGGLMGYSPGESISGCGSTG 1
2 GAQLGTGDGHTVVQSCTLGDSHSGTSGIQQQ 1
2 GYCQASSILHYAHGDNQQSHLLQA 1
2 GRTALGTGISAGKRPNPEEETQSVGPKVQRQSTN* 0

>CRY1_sylBor Sylvia borin (warbler) AJ632120 15381765
0 MGVNAVHWFRKGLRLHDNPALRECIQGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITPEVMKKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEE 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPESIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNPNGNGNGGLMGYSPGESISGCGSTG 1
2 GAQLGAGDGHSVVQSCALGDSHTGTSGVQQQ 1
3 GYCQASSILHYAHGDNQQSHLLQA 1
2 GRTALGTGISAGKRPNPEEETQSVGPKVQRQSTN* 0

>CRY1_taeGut Taeniopygia guttata (finch) XM_002196518
0 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 0
0 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITPEVMKKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 GMKVFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPESIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNPNGNGNGGLMGYSPGESISGCGSTG 1
2 GAQLGTGDGHSVVQSCALGDSHTGTSGIQQQ 1
2 GYCQASSILHYAHGDNQQSHLLQA 1
2 GRTALGTGISAGKRPNPEEETQSVGPKVQRQSTN* 0

>CRY1_melUnd Melopsittacus undulatus (budgerigar) AGAI01062111
1 RYLPVLRGFPAKYIYDPWNAPESIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL
GLLATVPSNPNGNGNGGLMGYSPGESISGCSSAGG
GAQLGTGDGHTVVQPCALGDSHTAGASGIQQQ
GYCQASSILHYAHGDNQQSHLLQAG
VGTGISAGKRPNPEEETQSVGPKVQRQSTN* 0

>CRY1_anoCar Anolis carolinensis (lizard) XM_003220923
0 MGVNAVHWFRKGLRLHDNPALREVIQGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYELDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEIPVETITAEVMSKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPDGVQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQMYQQLSRYRGL 1
2 GLLASVPSNGNGNGNGGLMGYSTGENIPGCTNTN 1
2 GSQMGMNEGHIGNVQACTMGESHTGTSGIQQQ 1
2 GYSQGSGILLYSHGDNQKTHSAQKGRISLGT 1
2 GVCTGKRPSPEVETQSVGPKVQRQSSN* 0

>CRY1_podSic Podarcis siculus (wall lizard) DQ376040 16809482
0 MGVNAVHWVRQGLRLPDNRALREVIQGADTARCVYILDPSFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNITKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITAEVMSKCTTPVSDDHDEKCGVPSLEEL 1
2 GFDTGGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARRAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGVQKVAKCVIGVNYPKPMVNHTEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPLMEWNVIVLMGYHQGTLLVYHAS 1
2 GSQMGTNEAHTGSVQTCTLGESHTGTSGIQQQ 1
2 GYPQGSDILHYAHGEGQKTHLIQQGRASLVA 1
2 GVCTGKRPNPEEETQSIGPKVQRQSSK* 0

>CRY1_pytMol Python molurus (python) AEQU010547455 
0 MGVNSVHWFRKGLRLHDNPALREVIQGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFk 0
0 EWNISKLSIEYDSEPFGKERDAAIKKLATEAGLEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITAEVMSKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLER 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0 
2 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPILRGFPAKYIYDPWNAPEGVQKAAKCIIGINYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL
2  1
2 GAQMGTSEGHTGNVQACTLGETHTGTSGIQQQ 1
2 GYSQGNSGILHYAHGDSQKTLLMQ 1
2 GRTSLSVGVCTGKRPNPEEGIQSIGPKVQRQSSN* 0

>CRY1_chrPic Chrysemys picta (turtle) AHGY01469963 AHGY01469969
0 MGVNAVHWFRKGLRLHDNPALRECIQGADSVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNIAKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISRMEPLEMPVETITAEVMEKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTDGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNRSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVSFGRRTDPNGDYIR 2
1 RYLPILRGFPAKYIYDPWNAPESIQKAAKCVIGVHYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLATVPSNP  NGNGGLMGYSPGENISGCSSAS 1
2 GAQMGSNDGHTVGVQTCSLEDSHAGSSGIQQH 1
2 GYSQGNSIVHYAQGDHQQSHLLQQG 1
2 GRTVSTGISTGKRPNPEKETQSIGPKVQRQSTN* 0  


>CRY1_xenTro Xenopus tropicalis (frog) NM_001087660 11533577 final four exons confirmed by many ESTs
0 MGVNAVHWFRKGLRLHDNPALRECIQGADTVRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWKITKLSIEYDSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDK 2
1 IIELNGGQPPLTYKRFQTLISKMDPLEIPVETITAEVMEKCTTPVSDDHDEKYGVPSLEEL 1
2 GFDTEGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASTTGLSPYLRFGCLSCRLFYFKLTDLYKK  0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMDGNPICVQIPWDRNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGKRTDPNGDYIR 2
1 RYLPILKGFPPKYIYDPWNAPETVQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGL 1
2 GLLASVPSNPNGNGNGGLMSYSPGESMSGCSNNG 1
2 GGQMGVNEGSSASNPNANKGEVHPGTSGLQ 1
2 GYWQGSSILHYSHSDSQQSYLMQ 1
2 ARNPLHSVVSSGKRPNPEEETQSIGPKVQRQSSH* 0

>CRY1_latCha Latimeria chalumnae (coelocanth) 
0 MGVNAIHWFRKGLRLHDNPALREAIQGGDCIRCVYILDPWFAGSSNVGINRWR 2
1 FLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFK 0
0 EWNISRLSFEYDSEPFGKERDAAIKKLASEAGVEVIVRITHTLYDLDR 2
1 IIELNGGQPPLTYKRFQTLISRMEPLDLPVETINSEVMGNCSTPVSDDHDEKYGVPSLEEL 1
2 GFDTEGLPSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPEGVQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGM 1
2 GLLASVPSNPNGNGGLGCSLAENIPVCNSAA 1
2 GAQMGGDDGHKVSVLAYTQGDSRAGEIEMQQQ gcyi* 1
2  1
2  * 0

>CRY1_danRer Danio rerio (zebrafish) NM_001077297
0 MVVNTVHWFRKGLRLHDNPSLRDSILGAHSVRCVYILDPWFAGSSNVGISRWR 2
1 FLLQCLEDLDASLRKLNSRLFVIRGQPTDVFPRLFK
0 EWNINRLSYEYDSEPFGKERDAAIKKLANEAGVEVIVRISHTLYDLDK 2
0 IIELNGGQSPLTYKRFQTLISRMEAVETPAETITAEVMGPCTTPLSDDHDEKFGVPSLEEL 1
2 GFDTEGLSSAVWPGGETEALTRLERHLERK 0
0 AWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYRK 0
0 VKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMK 0
0 VFEELLLDADWSVNAGSWMWLSCSSFFQQFFHCYCPVSFGRRTDPNGDYIR 2
1 RYLPVLRGFPAKYIYDPWNAPESVQKAAKCIIGVHYPMPMVHHAEASRLNIERMKQIYQQLSCYRGL 1
2 GLLAMVPSNPNGNGENSTSLMGFQTGDMTKEVTTPS 1
2 GYQMPPTSQGEWHGRTMVYSQGDQQTSSIMTSQ 1
2 GFGNNGSTMCYRQDAQQIT 1
2 GRGLHSSIIQTSGKRHSEESGPTTVSKVQRQCSS* 0

Vertebrate CRY2 reference sequences

(more coming shortly)

>CRY2_hetGla  Heterocephalus glaber (mole-rat) EHA99865
MAAAVGTGTGAAPTPATGAEGACSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRW
RFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFK
EWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDR
IIELNGQKPPLTYKRFQAIISRMELPKKPVGAVSSQQMKSCRAEIQENHDDTYGVPSLEEL
GFPTEGLGPAVWQGGETEALARLDKHLERK
AWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKK
VKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVR
VFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIR
RYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRYRGL
CLLASVPSCVEDLSHPVAEPTLSQAGSSSSTG
PRSLPDGPASPKRKLEAAEEPPGEEL
SKRARVAELPAPEPTSKDA*

Insect photolyases and cryptochromes

>CRY1_droMel Drosophila melanogaster (fruit fly) cryptochrome 3TVS CG3772
mATRGANVIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAGTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRL
LVFEGEPAYIFRRLHEQVRLHRICIEQDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMF
LHTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVYGDNMGFLAKINWRGGETQALLLLDERLKVE
QHAFERGFYLPNQALPNIHDSPKSMSAHLRFGCLSVRRFYWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTM
SVNNPNYDRMEGNDICLSIPWAKPNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHGL
QHFLKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLDPDGTYIKQYVPELMNVPKEFVHEPWRMSAEQQE
QYECLIGVHYPERIIDLSMAVKRNMLAMKSLRNSLITPPPHCRPSNEEEVRQFFWLADvvv

>CRY64_droMel Drosophila melanogaster (fruit fly) 6-4 photolyase 3CVW CG2488-RA (phr6-4) length=540
MDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGKYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDA 
AVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIW 
VARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQE
GWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRI
VKHEVVHKENIKRMGAAYKVNREVRTGKEEESSFEEKSETSTSGKRKVRRATGSAPKRKR

>CPD_droMel Drosophila melanogaster (fruit fly) thymidine dimer photolyase
MHEDDLKSQLTIARNEINNLRQQVRNLQHVQRKDIETITRLLQDFRCEGCANNNKSAKDKVAGEKQEHQHQQQTQLIESPYRYTVMFTLASYWRESFKIV
LPLQAMKRTKAQKAGPSKKAAKNEKASSEPKSDQESSDEEASTSKALLVSKPDYQNFEQFLTHLEHQRVCTAANIQEFSFRKKRVRVLSKTEDVKESSLG
GVVYWMSRDGRVQDNWALLFAQRLALKLELPLTVVFCLVPKFLNATIRHYKFMMGGLQEVEQQCRALDIPFHLLMGSAVEKLPQFVKSKDIGAVVCDFAP
LRLPRQWVEDVGKALPKSVPLVQVDAHNVVPLWVASDKQEYAARTIRNKINSKLGEYLSEFPPVVRHPHGTGCKNVNTVDWSAAYASLQCDMEVDEVQWA
KPGYKAACQQLYEFCSRRLRHFNDKRNDPTADALSGLSPWLHFGHISAQRCALEVQRFRGQHKASADAFCEEAIVRRELADNFCFYNEHYDSLKGLSSWA
YQTLDAHRKDKRDPCYSLEELEKSLTYDDLWNSAQLQLVREGKMHGFLRMYWAKKILEWTATPEHALEYAILLNDKYSLDGRDPNGYVGCMWSIGGVHDM
GWKERAIFGKVRYMNYQGCRRKFDVNAFVMRYGGKVHKKK