RetrogeneDB ID: | retro_ecab_142 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:123714474..123714869(+) | ||
| 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_142
GAGAAAAGAGATCAGTGTAATAAAAATATTTTAAGAAAACATTTTCCAAATTTGATGAAAGATATAAACACACAGATTCA
AGAAGCTCAGCAAACATGCAAACAAAATAAATACCAAGAAATCTATGACCAGACACACACTAATAAAATTTTAGAAAACT
GAAGATAAAAATATCTCGAAAGGAACCAGAAAAATTTAGCATTACTTATAGGGGGAAAAGTGTTCAAATGACTGTGAATT
TCTCTTCAGAAAACAAGCAAGCCAGAAGGAAGTGGAACATTTTTAAAGTACTGAAAGAAAAGAACCTTCAACCCAGAATT
CTACATCCAGCAAAAATATTCTTTGGAGATGAAAGTGAAATAAAGATATTCTTAGATGAAGGAAAACTAAGAGAA
ORF - retro_ecab_142 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.11 % |
| Parental protein coverage: | 55.19 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EERDKEAENRVAENFPNLKKETDIHIQEAQRTPK-KISPKRATPRHIIIKISKMNDKERIPRAARQK-KI |
| E.RD....N.....FPNL.K.....IQEAQ.T.K.KI..K....RH..IK..K..DK..I....R....I | |
| Retrocopy | EKRDQCNKNILRKHFPNLMKDINTQIQEAQQTCK>KINTKKSMTRHTLIKF*KTEDKN-ISKGTRKI>SI |
| Parental | SYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRD |
| .Y.G......V.FS.E..QARR.WN.IFK.LK.KNLQPRIL.PAKIFF..E.EIK.F.D..KLR. | |
| Retrocopy | TYRGKSVQMTVNFSSENKQARRKWN-IFKVLKEKNLQPRILHPAKIFFGDESEIKIFLDEGKLRE |
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_142 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_142 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_142 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,
|