RetrogeneDB ID: | retro_ecab_540 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 20:29304064..29304708(+) | ||
| 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_540
ATAACTGAACTGGAAAATACATTAGAGGGGTTCAACAGCAGACTGGATGAAGTAGACACACAAATCAGTGACCTGGAAAA
TAAAGCAATGTATCTCACCCAGACAGAGTGGAAAAATGAAAAAGAATTTTAAAAAGTAGAGATACCTTAAGACACCTCTG
GGACAACATCAAGTAGAATAATGTTTGCATGATAGGGGTCCCAGGAGGAGAAAAGTCCAGAAAAATTAATTGAATGGCTG
AAAACTTCCCTAATGGGAGAAGGGAAACAGACATCCAGGTTCAGGAAGCCCAGAGAGTTCCAAACAAGATGAACTCAAAG
AGAAACACATCAAGACACATTATAATTAAAATGGTAAAAGTTAAGGATAAAGAGAGAATCTTAAGAGCAGCTAGAGAAAA
AACAACTTATTATGTACAAGGGAAACCCCAAAAGGCTACCAGCAGATTTTTCAGCAGAAACTTTACAGAACAGAAAGAAG
TGGCATGACATAGTCAATGTGCTGAAAGGAAAAAACTTCCACCAGGAACTCTCTACCCGGCAAGGTTATCATTCAGAATT
GAAGGAGAGATTAAAAGTTTTCCAGATAAGCAAAAGCTAAAGCAGTTTATCACCATTAAGCCAGCCTTACAAGAAATGTT
AAAG
ORF - retro_ecab_540 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.63 % |
| Parental protein coverage: | 96.88 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | ITEKKSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEK-RIRQNENSLRELWDNIKCANIHVIGVPE |
| ITE....L.GFNSR...V...I..L.......T..E.K.EK.RI......LR.LWDNIK..N...IGVP. | |
| Retrocopy | ITELENTLEGFNSRLDEVDTQISDLENKAMYLTQTEWKNEK<RILKSRDTLRHLWDNIK*NNVCMIGVPG |
| Parental | ERQRGRKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAARE-RQ |
| .....RK......AE.FPN.R.ETD.QVQEAQRVPNK...KR.TSRHIIIKM.K.KDKERIL.AARE..Q | |
| Retrocopy | G-EKSRKI--N*MAENFPNGRRETDIQVQEAQRVPNKMNSKRNTSRHIIIKMVKVKDKERILRAARE>KQ |
| Parental | QVTYKGKPIRLSVDFSAKTLQVRREWHDIFKV-KEKN-LQPRILYPARLSFTMEGEIKSFQDKQKLKEFI |
| ...YKG.P.RL..DFSA.TLQ.R..WHDI..V.K.KN.L.P..LYPARLSF..EGEIKSF.DKQKLK.FI | |
| Retrocopy | LIMYKGNPKRLPADFSAETLQNRKKWHDIVNVLKGKN<LPPGTLYPARLSFRIEGEIKSFPDKQKLKQFI |
| Parental | TKKPILQEMLK |
| T.KP.LQEMLK | |
| Retrocopy | TIKPALQEMLK |
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_540 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_540 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_540 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,
|