RetrogeneDB ID: | retro_ecab_934 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 7:66274912..66275602(+) | ||
| Located in intron of: | ENSECAG00000021733 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000005242 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_934
AATAAGAATTTGAACAAAGAGAGAGAAAATATAACAAAGCACCAAACAGAAATCACAGAGCTAAGAAATACAGTAACGGA
ACTGAAAAATACAGTAGAGGGGTTCAAAAGCAGATTAGATGAAGCAGAAGAAAGGATCACCAAACTCAAAGACAGGGCGG
TGGAATTCATCCAATCAGAACAACAAAAAGAAAAAAGAATGAAAAAGAGTGAAAACAGCTTAAGGGACTTAAGGCACAAT
ATCAAATGGACTAATATTCACCATATAGAGGCCCTAGAAGGAGAAGAGAGAGAGAAAGGGGCAGAAAACTTATTTGAAAA
AATAATGGCAGAAAATTTCTTTATTCTGGGGAAGGAAACAGACAACCACATCCAGGAAGCTCAGAAAGTTCCAAATAAGA
TGAATGTAAAGAGACCCACACTAAGACACATAATTAAATTGTCAAAAGTTAAAGACAAGGAACCTTAAAAGCAGCTAGAG
AAAAACAACTTGTTATGTACAAAGGAGCCCCCATAAAAAATCAGCAGATTTTTCAGCAGCAATTTTGCAAGCCAGAAGGA
AATGGCATGATACATTCAAAGGGCTGAAAGAAAAAACTGCCAACCAAGAATGCTCTACCTGGCAATGCTGTCCTTCAGAA
CTGAAGAGGAGATAACGAGTTTTCCAGACAAGCAAAAGCTGAAGGAGTTC
ORF - retro_ecab_934 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.91 % |
| Parental protein coverage: | 98.31 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SENFSKETENIRKYQIEVTELKNTPTELKNTIEGFKSRLDDTEERISGLEDRAVELIQSELSTQNRLEDL |
| ..N..KE.ENI.K.Q.E.TEL.NT.TELKNT.EGFKSRLD..EERI..L.DRAVE.IQSE.......... | |
| Retrocopy | NKNLNKERENITKHQTEITELRNTVTELKNTVEGFKSRLDEAEERITKLKDRAVEFIQSEQXXXXXXXXX |
| Parental | APSPKDCADSMRKCSIRTIGVQEGEEKEDGAESVLKEIIAENFPNLGDEREMCVEEVFRSPRYVNVKRPT |
| ..S..D.........I..I...EGEE.E.GAE.....I.AENF..LG.E......E....P...NVKRPT | |
| Retrocopy | XXSLRDLRHNIKWTNIHHIEALEGEEREKGAENLFEKIMAENFFILGKETDNHIQEAQKVPNKMNVKRPT |
| Parental | ARHIVVKLAKMNDKE-RILRAARLKKITYKGTPI-RLSVDFSAETLQARTDWNDIFKTLKD-KNLQPRIL |
| .RHI..KL.K..DKE.....A.......YKG.PI...S.DFSA..LQAR..W.D.FK.LK..KN.QPR.L | |
| Retrocopy | LRHI-IKLSKVKDKE<TLKAAREKQLVMYKGAPI<KKSADFSAAILQARRKWHDTFKGLKE<KNCQPRML |
| Parental | YPAKISFRYEGEIKSFPEKQKLRDF |
| Y.A..SFR.E.EI.SFP.KQKL..F | |
| Retrocopy | YLAMLSFRTEEEITSFPDKQKLKEF |
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 | 0 .00 RPM | 0 .00 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 0 .00 RPM |
| SRP021940_embryo | 0 .00 RPM | 0 .00 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 0 .05 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 0 .03 RPM |
| SRP021940_testis | 0 .00 RPM | 0 .00 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_934 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_934 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_934 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000005242 | 2 retrocopies |
retro_ecab_192, retro_ecab_934 ,
|
| Equus caballus | ENSECAG00000006639 | 4 retrocopies |