RetrogeneDB ID: | retro_acar_100 | ||
Retrocopy location | Organism: | Anole lizard (Anolis carolinensis) | |
| Coordinates: | 3:156802498..156804194(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSACAG00000002154 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CROT | ||
| Ensembl ID: | ENSACAG00000016327 | ||
| Aliases: | None | ||
| Description: | carnitine O-octanoyltransferase [Source:HGNC Symbol;Acc:2366] |
Retrocopy-Parental alignment summary:
>retro_acar_100
ATGGCTGACCATTCTGAAGAGTGCACATTTCAATACCAGAGTTCTCTTCCTTCATTGCCAGTTCCTGCTCTTGATGAATC
ATTACAGAAATACCTCGATTCAGTGAGACCTTTCCTAAAGGAGGAAGAATTTCAGCAAACTCAGGACATAGTAGAAAGAT
TTGAAAATGGAATTGGAAAGGAACTGCATCAAAAATTATTTGAAAGAGCAAAAGTGAAGTGGAATTGGCTTGAGGAATGG
TGGCTCAATGTAGCCTATCTCGAAGCCCACTTATCAACACAAATCTATTATAATTTTGGAGGCCCAGGTCCTTACCTTGA
ACACTTCTGGCCAATGAAAGAAGGGACTCAGATAGAAAGAGGCTCCATAACTATATGGATTTCTTTGAAATTCTGGGAAC
TACTGAGAACAGAAAAGTTGCGTGTCCACAAATCAAATAATATGCCTCTGGATATGAATCAGTTCCGAATGCTGTTTTGC
ACTTGCATGATTCCAGGAACTGTGCAAGATTCAATTGCCAATTATTTCAGGACAGAGAGTGAAGGTGAATGCCCATCTCA
TTTGGTAGTGCTGTGCCGAGGTCGAATTTTTGCATTTGATGGGGTACATGATGGCCATATATTAACCCCACCAGAGATTT
GTAGGCAGCTTTACTACATCCAAGAGATATGTCACAATGAACCTAAGGGACCTGGACTGGCTGCATTAACCTCTGAGTAA
AGAACCCCATGGGCAAAGACACGTGAATATCTTATCAACCTAGATACAAAGAATTTGCTCCATTTGGAAAAAATACAGAA
CAGCTTATTTGTGATCTCCTTAGATGAAGCAAGTCCCCAAGCCACTTCTGAAGATTATTCAGAGGTCACCAAGTTGTCAC
CAACAGGCGATCCAACATTAAGTTCGGGAGACAAATCCTATAACAAGATTATGTTTTTGAATGGATTATTTGGCTCAAAT
TGTGATCACTCTCCTTTTGATGCCATGGTTTTGGTTGTCTTCTGTTCTTTTATTGACTCCAAAATCATCGAATTAGAGGG
AAAATGGAAGGGATCAGAAAGAGTGCGGGATATCCCTTGGCCAGAGGAGCTTTTGTTCAGTTTGGATCAGAAAGTGCTAA
AAGACATTGCTCATGCTAAGGAGCAGTATGAAAAGAAGACACCTGATGTAGAATTGGTGAATTATGCTTTTACTTTCTTT
GACAAAGCTCTGATAAAGAAACAGAAGCTTTATCCTGATATATTCGTTCAGCTTGCTCTTCATGGCTTATTACTGACATC
ATGGACACCCAGGTTGCTGCTATGAAACTGCTACAACCAGACCCTATTACCATGGCCTCATAGAAACTATGCGGCCCTGC
ACCATAGAAGCAGTTGAATGATGTAAATCCATGCTCGATCCAACTTTTAATATCGGCCAACGAAAGCACCTTATGCTGAA
GGCCTTTGCAAAGCACCATAAACGGATGAAAGAGTATGAAATTGGAAAAGGATTTGGCTGTCACCTCTTAGGCCTTCGGT
TTCTCTCCAAAGAGCACAGCCATCCTATGCCTGAAATCTTCCTGAATACTGCTTTCAGTAGAAGTGGAGGAGGTGAAAAC
TTTGTTCTTTCCACTAGCTTGGTAGGCTACACAAGAGTTGGGGGAGCTGTTGTTCCAATAGTATACCATGGTTATGGCTT
TTTCTACAGAATTAGA
ORF - retro_acar_100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.3 % |
| Parental protein coverage: | 91.44 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VTDHSEERTFQYQSSLPSLPVPALDESLQKYLDSVRPFLKEEEFQRTQDIVKRFENGIGKELHQKLLERA |
| ..DHSEE.TFQYQSSLPSLPVPALDESLQKYLDSVRPFLKEEEFQ.TQDIV.RFENGIGKELHQKL.ERA | |
| Retrocopy | MADHSEECTFQYQSSLPSLPVPALDESLQKYLDSVRPFLKEEEFQQTQDIVERFENGIGKELHQKLFERA |
| Parental | KVKRNWLEEWWLNVAYLEARLPTQIYYNFGGPGPYLEHFWPMKEGTQIERGSITVWISLKFWELLRTEKL |
| KVK.NWLEEWWLNVAYLEA.L.TQIYYNFGGPGPYLEHFWPMKEGTQIERGSIT.WISLKFWELLRTEKL | |
| Retrocopy | KVKWNWLEEWWLNVAYLEAHLSTQIYYNFGGPGPYLEHFWPMKEGTQIERGSITIWISLKFWELLRTEKL |
| Parental | RVHKSNNTPLDMNQFRMLFCTCKIPGIVQDSIANYFRTESEGECPSHLVVLCRGRIFAFDGVHDGHILTP |
| RVHKSNN.PLDMNQFRMLFCTC.IPG.VQDSIANYFRTESEGECPSHLVVLCRGRIFAFDGVHDGHILTP | |
| Retrocopy | RVHKSNNMPLDMNQFRMLFCTCMIPGTVQDSIANYFRTESEGECPSHLVVLCRGRIFAFDGVHDGHILTP |
| Parental | PEICRQLYYIQERCHNEPKGPGLAALTSEERTPWAKTREYLINLDPKNLLHLEKIQSSLFVISLDEASPQ |
| PEICRQLYYIQE.CHNEPKGPGLAALTSE.RTPWAKTREYLINLD.KNLLHLEKIQ.SLFVISLDEASPQ | |
| Retrocopy | PEICRQLYYIQEICHNEPKGPGLAALTSE*RTPWAKTREYLINLDTKNLLHLEKIQNSLFVISLDEASPQ |
| Parental | ATPEDYSEVTKLSLTGDPTLRWGDKSYNKIMFSNGLFGSNCDHSPFDAMVLVVFCSFIDSKIIELEGKWK |
| AT.EDYSEVTKLS.TGDPTL..GDKSYNKIMF.NGLFGSNCDHSPFDAMVLVVFCSFIDSKIIELEGKWK | |
| Retrocopy | ATSEDYSEVTKLSPTGDPTLSSGDKSYNKIMFLNGLFGSNCDHSPFDAMVLVVFCSFIDSKIIELEGKWK |
| Parental | GSERVRDIPWPEELLFSLDQKVLKDVAHAKEQYEKKTSDVELVNYAFTSFGKALIKKQKLHPDIFVQLAL |
| GSERVRDIPWPEELLFSLDQKVLKD.AHAKEQYEKKT.DVELVNYAFT.F.KALIKKQKL.PDIFVQLAL | |
| Retrocopy | GSERVRDIPWPEELLFSLDQKVLKDIAHAKEQYEKKTPDVELVNYAFTFFDKALIKKQKLYPDIFVQLAL |
| Parental | -QLAYYRHHGHPGCCYETATTRRYYHGRTETMRPCTIEALEWCKSMLDPAFTLGQRKHLMLKAFAKHHKL |
| ....Y..H.GHPGCCYETATTR.YYHG..ETMRPCTIEA.E.CKSMLDP.F..GQRKHLMLKAFAKHHK. | |
| Retrocopy | >MAYY*HH-GHPGCCYETATTRPYYHGLIETMRPCTIEAVE*CKSMLDPTFNIGQRKHLMLKAFAKHHKR |
| Parental | MKECENGKGFDRHLLGLLLLSKEHSLPMPEIFLDPAFSRSGGGGNFVLSTSLVGYTRVGGAVVPMVHHGY |
| MKE.E.GKGF..HLLGL..LSKEHS.PMPEIFL..AFSRSGGG.NFVLSTSLVGYTRVGGAVVP.V.HGY | |
| Retrocopy | MKEYEIGKGFGCHLLGLRFLSKEHSHPMPEIFLNTAFSRSGGGENFVLSTSLVGYTRVGGAVVPIVYHGY |
| Parental | GFFYRIR |
| GFFYRIR | |
| Retrocopy | GFFYRIR |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP009831_adrenal | 0 .53 RPM | 24 .81 RPM |
| SRP009831_brain | 0 .14 RPM | 19 .36 RPM |
| SRP009831_dewlap | 0 .38 RPM | 78 .47 RPM |
| SRP009831_embryo | 0 .95 RPM | 51 .30 RPM |
| SRP009831_heart | 0 .47 RPM | 32 .63 RPM |
| SRP009831_liver | 0 .37 RPM | 80 .86 RPM |
| SRP009831_lung | 0 .30 RPM | 68 .46 RPM |
| SRP009831_ovary | 0 .50 RPM | 69 .92 RPM |
| SRP009831_skeletal_muscle | 0 .25 RPM | 37 .91 RPM |
Anolis carolinensis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_acar_100 retrocopy.
Anolis carolinensis was not studied using FANTOM5 data.
retro_acar_100 was not experimentally validated.
Retrocopy orthology:
Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000016327 | 1 retrocopy |
retro_acar_100 ,
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