RetrogeneDB ID: | retro_ecab_391 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 17:24750890..24751512(+) | ||
| 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: | ENSECAG00000019846 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_391
AAAAATTCAACAGAGGGTTTCAACAGCAGACTAGATGAAGTGGAAGAAAGGATCAGTGAACTCGAAGACAGGGCAGTAGA
ATCCATTTAAACAGAGGAGCAAAAAGAAAAAAGAATGAAAAAGAGTGAATACAGCTTAAGGGACTTATGGGACAACATCA
AGTGGACTAATATTCACTTTGTAGAAGTCCCTGAAGGAGAGGAGAGCTTACGTGAAGAGATAATGGCTGAAAACTTCCCT
AACCTGGGGAAAGTAACAGACATCCAGATCCAGGAAGTCCAGACAGTTACAAATAAGATAAATCTGACAGACCCACACCA
AGACTCATTATACTTAATCTGTCAAAAGTTAAAGGAGAGATTATTAACAGTAACAAGAGGAAAACTACTTGTTGCATACA
AGGGAACTCCCACAAGACCATCAGCAGATTTTTCAGCAGAAATTTTGCAGGTCAGAAGGGAGTGGCATGATATATTCAAA
GTACCGAAACATAAAAACTGCCAGCCAAGAATACTCTACCTGGCCAAGTTTTACTTTAGAATTGAAGGAGAGAGAGAGTT
TTCCAGAGACGCAAAAGCTGAAGGAGTTCATCACTGGACAAGCCTTAGAAGAAATGTTAAAG
ORF - retro_ecab_391 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.63 % |
| Parental protein coverage: | 95.09 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVIGVPEERQRG |
| K.S..GFNSR...VEERI..L.D...E....E..........E.SLR.LWDNIK..NIH...VPE..... | |
| Retrocopy | KNSTEGFNSRLDEVEERISELEDRAVESI*TEEXXXXXXXXSEYSLRDLWDNIKWTNIHFVEVPEGEE-- |
| Parental | RKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAARERQQVTYKG |
| ..L.EEI.AE.FPNL.K.TD.Q.QE.Q.V.NK.....P..........K.K..ER.L...R....V.YKG | |
| Retrocopy | -SLREEIMAENFPNLGKVTDIQIQEVQTVTNKINLTDPHQDSLYLICQKLK--ERLLTVTRGKLLVAYKG |
| Parental | KPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQ-DKQKLKEFITKKPIL |
| .P.R.S.DFSA..LQVRREWHDIFKV.K.KN.QPRILY.A...F..EGE...F....QKLKEFIT....L | |
| Retrocopy | TPTRPSADFSAEILQVRREWHDIFKVPKHKNCQPRILYLAKFYFRIEGE-REFS>ETQKLKEFITGQ-AL |
| Parental | QEMLK |
| .EMLK | |
| Retrocopy | EEMLK |
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 .00 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_391 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_391 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_391 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019846 | 8 retrocopies |
retro_ecab_1033, retro_ecab_391 , retro_ecab_528, retro_ecab_531, retro_ecab_540, retro_ecab_574, retro_ecab_615, retro_ecab_918,
|