RetrogeneDB ID: | retro_ecab_367 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 16:73233929..73235092(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000023737 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DLGAP5 | ||
| Ensembl ID: | ENSECAG00000008655 | ||
| Aliases: | None | ||
| Description: | discs, large (Drosophila) homolog-associated protein 5 [Source:HGNC Symbol;Acc:16864] |
Retrocopy-Parental alignment summary:
>retro_ecab_367
CCGGCCACAGGAGCGACGCGTGATAAAGAAACAGAAAGAAAAGTACCCAATCAAGGAAGGCCTGCCAAAAAGATAGAAAG
AAAACCTGGCAAGGTCGTTTCCTTTAAAGTTGATAGTGAAGAAAATACTTTGGAGTCACAAACCAATGTGACAAACGGAA
CGGATCCAGATGGAGTCTTATCAAAAATGGAAAAGTTACCTAAGTCAAATCCTGCAGCAGTGAAAGGGAGGCCATCCTTC
GCACCAGTAGATTTCGTATTTCGGCCTCCAGATGGTCTGAAGAGCTATGAGATAACACCTAGGAAGCCCACAAAAACCAC
TGCGTGGACGCCCGCTTACAGCTGCAGCTCTTTAAACACGGAAGTTGATAAGGCTCTAGAAGCAACAAAAGAAATTTTGG
CACAGAAATGTAAACCTTCAGCACATCAAGATTACGATGAATTTCGCCGTCCTTTGCGCTCCCTAGCAGTCGGGAGCACA
GATCGTGTCTTAAAGAAAAATGAAACTACTACTGAAAATCTACATGGCCTTCCAATAAAAGAAGTCCCATCACTTGAAAT
AAATGAGGATCAGACATCTCAGCAACCACACGTGCTGTATTTCAGAAATATTCTCCAGTCAGAAACTGAAAAACTAACTT
CACACTGCCTTGAGTGGGAAAGGAAGCTTGAATTGGACATTCCAGATGAAGCCAAAGACCTTATTCGCCTGGCAGTTGGT
CAAACAAGACTCCTTATGAAAGAAAGGTTCAAACAGTTTGAAGAACTGGTGGACAATTGTGACTATAAACGAGGAGAAAA
GGATACCACCTGTACAGACCTGGATGGCTTTTGGGATATGGCTAGCCTTCAGATATGGGATGTAAACCAAAAATTCAACA
ATCTGACCAAACTGGAGGAGTGTGAATGGCAAAACAATAATAATACAAGCAAAAAAGTCTTTCAGAAAAAAGTTGTTTCG
GGTATAGCAAGTAAACCAAAACAGGACGATGCTGGGAGAATTGCAGCCAGAAGTCGCCTCGCTGCTGTGAAGAAGGCAGT
GAGAGAGAGGATGCACGGGGAGAGCAGGCCGAGGCCGAGGGCTCTGCAGCGCCGAAGGAAGTTGATCAAATAGTGTTTGA
CGCTGGATTTTTTAGAATTGAAAGTCCCGTTAAATCGTTCTCA
ORF - retro_ecab_367 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.26 % |
| Parental protein coverage: | 61.98 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PATRAARDNETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQTIVTNGMDPDGVLSKMEKLPKTN |
| PAT.A.RD.ETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQT.VTNG.DPDGVLSKMEKLPK.N | |
| Retrocopy | PATGATRDKETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQTNVTNGTDPDGVLSKMEKLPKSN |
| Parental | PAAVKGRPSFAPVDFVFRPPDGLKSYEITPRTPTSTAAWTPTYSCSSLNTEVDKAPEATKETLAQKCKPS |
| PAAVKGRPSFAPVDFVFRPPDGLKSYEITPR.PT.T.AWTP.YSCSSLNTEVDKA.EATKE.LAQKCKPS | |
| Retrocopy | PAAVKGRPSFAPVDFVFRPPDGLKSYEITPRKPTKTTAWTPAYSCSSLNTEVDKALEATKEILAQKCKPS |
| Parental | AHQECDGWRRPLSSLAVGSTDRVLNKNETTTENLHGLPIKEVPSLEINEDQTSQPRHVLYFRSILQSETE |
| AHQ..D..RRPL.SLAVGSTDRVL.KNETTTENLHGLPIKEVPSLEINEDQTSQ..HVLYFR.ILQSETE | |
| Retrocopy | AHQDYDEFRRPLRSLAVGSTDRVLKKNETTTENLHGLPIKEVPSLEINEDQTSQQPHVLYFRNILQSETE |
| Parental | KLTSHCLEWERKLELDVPDEAKDLIRLAVGQTRLLMKERFKQFEELVDDCEYKRGEKDTTCADLDGFWDM |
| KLTSHCLEWERKLELD.PDEAKDLIRLAVGQTRLLMKERFKQFEELVD.C.YKRGEKDTTC.DLDGFWDM | |
| Retrocopy | KLTSHCLEWERKLELDIPDEAKDLIRLAVGQTRLLMKERFKQFEELVDNCDYKRGEKDTTCTDLDGFWDM |
| Parental | VSLQVRDVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSGLASKPKQDDAGRIAARSRLAAVKKAVRER |
| .SLQ..DVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSG.ASKPKQDDAGRIAARSRLAAVKKAVRER | |
| Retrocopy | ASLQIWDVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSGIASKPKQDDAGRIAARSRLAAVKKAVRER |
| Parental | MQ-RGEQAGAAGSAVPKEVDQIVFDAGFFRIESPVKSFS |
| M..RGEQA.A.GSA.PKEVDQIVFDAGFFRIESPVKSFS | |
| Retrocopy | MH<RGEQAEAEGSAAPKEVDQIVFDAGFFRIESPVKSFS |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 1 .77 RPM | 0 .06 RPM |
| SRP021940_cerebellum | 7 .58 RPM | 0 .31 RPM |
| SRP021940_embryo | 2 .17 RPM | 22 .45 RPM |
| SRP021940_placental_villous | 0 .72 RPM | 2 .26 RPM |
| SRP021940_synovial_membrane | 1 .65 RPM | 2 .31 RPM |
| SRP021940_testis | 1 .09 RPM | 16 .75 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_367 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_367 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_367 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000007001 | 1 retrocopy | |
| Equus caballus | ENSECAG00000008655 | 1 retrocopy |
retro_ecab_367 ,
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