RetrogeneDB ID: | retro_ecab_394 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 17:28633062..28633727(+) | ||
| 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_394
GAGAGAAAGAACACAATGAATGAGATTTTTTTTAAAAATCTAGAAACTTTAAAAAACAGAGCTGAAGTTATGGAGGACAG
ACTTAGTGATTTAGAGGACAGAAATATAGAAATGCAGGTGGAGAAGGAGCGAGAACTAAGACTTTTAAACAATGAAGAAG
TTCTTCAAGAAATATCCAACTCAATTAGGAAATGCAACATAAGGATTACAGGTATTCCAGAGAGAGAAAGGAGCAGAGAG
CTTGTTCAAAGAAATAATTAGAACTTCCCAAACCTGGGGAAAGAATTGGACTTACGAGTACATGAAGTCAATAGAACTCT
TAATTACATCAATGCAAAAGACCTTCTCCAAGGCATATAATAGTAAAACTGGCAAAAGTTAATGACAAAGAAAAAATATC
AAGAGCAGCAAGGCAGAAGAAAATAACCTACAAAGGAACCCTTATCAAACTTTCAACAGATTTCTTAGCAGAAACCTTAC
AGGCTAGGAGAGATTGGAATGATATATTCAAAATTCTGAAAGACAAAAACTTTCAGCAAAGAATACGCTATCCAGCAAAA
CTATCCTTCAGATACAATAGAGAAATAAAGGCTTTCCCAGTTTAACAAAAGTTGAGCGAGTTCATCACCACTAGACCTCC
CTTAAAAGAAATGAGGAAGGATGCC
ORF - retro_ecab_394 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.44 % |
| Parental protein coverage: | 92.53 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EMKNTTLEMK-SSLERLNSRVSDTHEQMSEIDERLEEISQAEQKKEKRIRQNENSLRELWDNIKCTNIRF |
| E.KNT..E.....LE.L..R........S....R..E..Q.E...E.R...NE..L.E....I...NIR. | |
| Retrocopy | ERKNTMNEXXXKNLETLKNRAEVMEDRLSDLEDRNIEM-QVEKERELRLLNNEEVLQEISNSIRKCNIRI |
| Parental | IGVPEGEERDKEAENRVAENFPNLKKETDIHIQEAQRTPKKISPK-RATPRHIIIKISKMNDKERIPRAA |
| .G.PE..ER..E...R...NFPNL.KE.D....E..RT...I..K.R..PRHII.K..K.NDKE.I.RAA | |
| Retrocopy | TGIPE-RERSRELVQRNN*NFPNLGKELDLRVHEVNRTLNYINAK<RPSPRHIIVKLAKVNDKEKISRAA |
| Parental | RQKKISYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRD |
| RQKKI.YKGT.I.LS..F..ETLQARRDWNDIFK.LKDKN.Q.RI.YPAK..FRY..EIK.FP..QKL.. | |
| Retrocopy | RQKKITYKGTLIKLSTDFLAETLQARRDWNDIFKILKDKNFQQRIRYPAKLSFRYNREIKAFPV*QKLSE |
| Parental | FVATSPPLQEILKKA |
| F..T.PPL.E..K.A | |
| Retrocopy | FITTRPPLKEMRKDA |
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_394 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_394 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_394 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,
|