RetrogeneDB ID: | retro_ecab_128 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:57249023..57249836(+) | ||
| Located in intron of: | ENSECAG00000000471 | ||
Retrocopy information | Ensembl ID: | ENSECAG00000008345 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CYP2R1 | ||
| Ensembl ID: | ENSECAG00000007597 | ||
| Aliases: | None | ||
| Description: | cytochrome P450, family 2, subfamily R, polypeptide 1 [Source:HGNC Symbol;Acc:20580] |
Retrocopy-Parental alignment summary:
>retro_ecab_128
TCAGCCTTTCCATGGATTGGCATCTTACCTTTTGGAAAACATCAACAGCTGCTTAGAAATGCAGCTGTGGCCTACGATTT
TTCTCCCCAGGCTTATTGAAAAAGTTCCTGGTGACAAAAAGCCTCAGTTGCCTCAGCATTTTGTTGGTGCTTATTTAGAT
GAGATGGATCAAGGTAAAAATGACCCATCGTCTGCTTTCTCCAAAGAAAAGCTAATTTTCTCTGTGGATGAACTCATCAT
TGCTGGAACCAAAACTATAACCAATGTGCTATGGTGGGCAGTTCTTTTCATGGCCCTTTATCCTAACATTCAAGGACGGG
TTCAGAAGGAGCTTGATTTAATTATGGGACCCAGTGGGAAGCCATCTTGGGATGACACATGCAAAATGCCTTATACTGAG
GCAGTTTTGTGTGAAGTTTTAAGATTCTGTAATATAGCGCCATTAGCGATTTTCCATGGAGCCTCTGTAGATGTAGTTGT
ATGTGGTGATTCCATTCCTAAAGGCAAAGCAGTTATTACAAATCTTTATTCTGTACACTTCAATGAAGAGTACTGGAGAG
ACCCAGAAGTATTCTATCCTGAGCAATTTCTGGACAGCAGTGGACTTTTTGCCGAGAAGGAAGCTTTGCTTCCTTTTTGC
TTAGGAAGAAGAGATGGTCCTGGAGAACAGCTGGCTCAGTGGAAATGTTCCTGTTTTTTACAGCATTGCTTCAGCTGTTT
CACTTGCATTCTCCAGATGAACTGGTTCCAAATCTGAAGCCCAGGTTAGGCATGACATGCCAACCGCAGCCTTACCTCAT
CTGTGCAGAAAGA
ORF - retro_ecab_128 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.85 % |
| Parental protein coverage: | 62.16 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | NAFPWIGILPFGKLQQLFRNADVVYEF-LSRLIEKVSVNRKPQLPQHFVDAYLDEMDQGQNDPSSTFSKE |
| .AFPWIGILPFGK.QQL.RNA.V.Y.F.L.RLIEKV....KPQLPQHFV.AYLDEMDQG.NDPSS.FSKE | |
| Retrocopy | SAFPWIGILPFGKHQQLLRNAAVAYDF>LPRLIEKVPGDKKPQLPQHFVGAYLDEMDQGKNDPSSAFSKE |
| Parental | NLIFSVGELIIAGTETTTNVLRWAILFMALYPNIQGQVQKEIDLIMGPSGKPSWDDKCKMPYTEAVLHEV |
| .LIFSV.ELIIAGT.T.TNVL.WA.LFMALYPNIQG.VQKE.DLIMGPSGKPSWDD.CKMPYTEAVL.EV | |
| Retrocopy | KLIFSVDELIIAGTKTITNVLWWAVLFMALYPNIQGRVQKELDLIMGPSGKPSWDDTCKMPYTEAVLCEV |
| Parental | LRFCNIVPLGIFHATSEDTVVRGYSIPKGTTVITNLYSVHFDEKYWRDPEIFYPERFLDSSGYFAKKEAF |
| LRFCNI.PL.IFH..S.D.VV.G.SIPKG..VITNLYSVHF.E.YWRDPE.FYPE.FLDSSG.FA.KEA. | |
| Retrocopy | LRFCNIAPLAIFHGASVDVVVCGDSIPKGKAVITNLYSVHFNEEYWRDPEVFYPEQFLDSSGLFAEKEAL |
| Parental | IPFSLGRRHCLGEQLAR-MEMFLFFTALLQRFHLHFPHELVPNLKPRLGMTLQPQAYLICAER |
| .PF.LGRR...GEQLA...EMFLFFTALLQ.FHLH.P.ELVPNLKPRLGMT.QPQ.YLICAER | |
| Retrocopy | LPFCLGRRDGPGEQLAQ<VEMFLFFTALLQLFHLHSPDELVPNLKPRLGMTCQPQPYLICAER |
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 .35 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP021940_embryo | 0 .00 RPM | 0 .66 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 0 .67 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 0 .33 RPM |
| SRP021940_testis | 0 .00 RPM | 10 .61 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_128 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_128 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_128 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000015305 | 1 retrocopy | |
| Equus caballus | ENSECAG00000007597 | 1 retrocopy |
retro_ecab_128 ,
|
| Ochotona princeps | ENSOPRG00000006268 | 1 retrocopy |