RetrogeneDB ID: | retro_ecab_237 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 10:34702976..34703478(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000009821 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_237
AGAAAAAAGAATAGTCTAAGGGACCACTGGGACAACAAGTGCATTAACATTCATATTATAGGTTTCCCAGAAGGAGAAGA
AAGAGACAAAGGGGCAAAGAATCTATTTGAAGGAATAATAGCTGAAAACTTTCCTAACCTAAGGAAGGAAACAGACATCA
AGGTACAGGAAGCACAGAGAACACCAAACAAGATAAACCCAAAGAGGCTCAAACCAAGACACATTATAAATAAAATGTCA
AGAATTAAAGAAAAAGAGAGAATCCTAAAAGCCATAATGGGCAACAAGTTACATACAAAGGAAATCCCATAAGGCTATCA
GCTGACTTCTCAGCAGAAACCTTATAAGCTAGAAGGGAGTAGCATGATATATTTAAAGTGCACAAAGGAAAGAACCTACA
GCCAAGGATACCCTACTGCCAAGTTTACCATTTGGAATGGAAGGAGAGACAAAGAGTTTCTTAGACAAGCAAAAAGTAAA
GGAGTTTATCACCAAGAAACCA
ORF - retro_ecab_237 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.31 % |
| Parental protein coverage: | 68.46 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QNENSLRELWDNIKCTNIRFIGVPEGEERDKEA----ENRVAENFPNLKKETDIHIQEAQRTPKKISPKR |
| ...NSLR..WDN.KC.NI..IG.PEGEERDK.A....E...AENFPNL.KETDI..QEAQRTP.KI.PKR | |
| Retrocopy | RKKNSLRDHWDN-KCINIHIIGFPEGEERDKGAKNLFEGIIAENFPNLRKETDIKVQEAQRTPNKINPKR |
| Parental | ATPRHIIIKISKMNDKERI-PRAARQKKISYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRIL |
| ..PRHII.K.S....KERI.P.........YKG.PIRLS..FS.ETL.ARR...DIFK..K.KNLQPRI. | |
| Retrocopy | LKPRHIINKMSRIKEKERI<PKSHNGQQVTYKGNPIRLSADFSAETL*ARRE*HDIFKVHKGKNLQPRIP |
| Parental | YPAKIFFRYE-GEIKSFPDNQKLRDFVATSP |
| Y..........GE.KSF.D.QK...F....P | |
| Retrocopy | YCQVYHLEWK<GETKSFLDKQKVKEFITKKP |
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 .00 RPM | 0 .00 RPM |
| SRP021940_embryo | 0 .00 RPM | 0 .00 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 0 .00 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 0 .00 RPM |
| SRP021940_testis | 0 .00 RPM | 0 .06 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_237 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_237 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_237 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000009821 | 7 retrocopies |
retro_ecab_137, retro_ecab_142, retro_ecab_237 , retro_ecab_394, retro_ecab_643, retro_ecab_731, retro_ecab_925,
|