RetrogeneDB ID: | retro_ecab_1114 | ||
Retrocopylocation | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:58975248..58975717(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CTHRC1 | ||
| Ensembl ID: | ENSECAG00000020399 | ||
| Aliases: | None | ||
| Description: | collagen triple helix repeat containing 1 [Source:HGNC Symbol;Acc:18831] |
Retrocopy-Parental alignment summary:
>retro_ecab_1114
CGTGATAGATTCAAAGGAAGAAAATGTGAAATGTTCAAGGGAAATTTTAGAGAAATCTAGCCACCTAACTATGAGCAGTA
TTCATAGGGTTCACATAACTATGACATAGGTCTCAGAAAACTTTCAGAGTGTACATTTACGTCGATGCATTCTAACACTG
CTCTAGGAGTATTGTTTAGTGGACCATTTTGACAAAAATGTAAAAATGCAAGCTGTCAGTAGTGGTATTTTTACATCGAG
TGGAGCTGAATGTACTGGACTCCTTCCCATGGGAGCCATAATAAATTTGGACCAAGGAATCCTTGAACTGAATTCAACAT
CAGTCTCCATCACACTTCTGCAGTAGAAGGAAGGCTCATCCAAGGAAAACAGAGTCAGGTAAATAGATGTTTTTATCTAA
GTTGGAACTTGTTCAGATTCATCAAAATAAAATTCTTATACATATTGGAATTTAGTGTTTGATGTCATT
CGTGATAGATTCAAAGGAAGAAAATGTGAAATGTTCAAGGGAAATTTTAGAGAAATCTAGCCACCTAACTATGAGCAGTA
TTCATAGGGTTCACATAACTATGACATAGGTCTCAGAAAACTTTCAGAGTGTACATTTACGTCGATGCATTCTAACACTG
CTCTAGGAGTATTGTTTAGTGGACCATTTTGACAAAAATGTAAAAATGCAAGCTGTCAGTAGTGGTATTTTTACATCGAG
TGGAGCTGAATGTACTGGACTCCTTCCCATGGGAGCCATAATAAATTTGGACCAAGGAATCCTTGAACTGAATTCAACAT
CAGTCTCCATCACACTTCTGCAGTAGAAGGAAGGCTCATCCAAGGAAAACAGAGTCAGGTAAATAGATGTTTTTATCTAA
GTTGGAACTTGTTCAGATTCATCAAAATAAAATTCTTATACATATTGGAATTTAGTGTTTGATGTCATT
ORF - retro_ecab_1114 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.59 % |
| Parental protein coverage: | 63.52 % |
| Number of stop codons detected: | 8 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RDGFKGEKGECLRETFEESWTPNYKQCSWSSLNYGIDLGKIAECTFTKMRSNSALRVLFSGSLRLKCRNA |
| RD.FKG.K.E.....F.E...PNY.Q.S..S.NY.I.L.K..ECTFT.M.SN.AL.VLFSG....KC.NA | |
| Retrocopy | RDRFKGRKCEMFKGNFREI*PPNYEQYS*GSHNYDIGLRKLSECTFTSMHSNTALGVLFSGPF*QKCKNA |
| Parental | CCQRWYF-TFNGAECSGPLPIEAIIYLDQGSPELNST-INIHRTSSVEGLCEGIGAGLVDIAIWVGTCSD |
| .CQ.WYF.T..GAEC.G.LP..AII.LDQG..ELNST...I......EG..........D..I.VGTCSD | |
| Retrocopy | SCQ*WYF>TSSGAECTGLLPMGAIINLDQGILELNSTSVSITLLQ*KEGSSKENRVR*IDVFI*VGTCSD |
| Parental | YPKGDASTGWNSVSRII |
| ..K....T.WN.V...I | |
| Retrocopy | SSK*NSYTYWNLVFDVI |
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 .30 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 1 .09 RPM |
| SRP021940_embryo | 0 .00 RPM | 16 .42 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 19 .39 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 44 .39 RPM |
| SRP021940_testis | 0 .00 RPM | 1 .34 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1114 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1114 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1114 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000020399 | 1 retrocopy |
retro_ecab_1114 ,
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