RetrogeneDB ID: | retro_ecab_528 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 2:112845580..112846199(-) | ||
| Located in intron of: | ENSECAG00000024339 | ||
Retrocopy information | Ensembl ID: | ENSECAG00000024427 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000019846 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_528
AACAGCAGAGCAGATGATACAAAAGAATGAATCAGTGAGTTGGACAAAAGAGCAGAGGAAATCACCAAAGCCAAACAGAA
AAAAGAAAAAATAATGAAAAAGAATGAGAACAGTATAAGGGACTTCTGGGACAACATCAAGCATAGTAACATCCACCTTA
TAGGTGTCCCAGAAGGTGAAGAGGAAGACAAAGGGGCTGAAAAATTATTTGAATAATAGCTGAAAACTTCCCTAACCAGG
AGAAGGAAACAGACATCCAGGTACAGGAAGCACAGAGAGTACCAAACAAGAGGAACCCAAAGAGGCCCACACCAAGACAC
ATTATAATTAAAATGTAAAGAATTAAAGTTAAAGAGAGAATCCTAAAAGCTGCAAGAGAAAAGCAACAAATTACATACAA
AGGAAATTCCATAAGGCTATCAGCTGACTTTTCAGCAAAAACTTCACAGGCTAGAAGGGAGGCACGATATATTCAAAGTG
CTGAAAGGAAAAAATCTGCAACCAAGAATACCCAGCAAGGTTATCATTCAGAATGGAAAGAGATAAAGAGCTTTCCAAAT
AGCAAAAACTAAAGGGGTTCATCACCACTAAACTGGTATTATAAGCAATGTTAAAGGGG
ORF - retro_ecab_528 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.02 % |
| Parental protein coverage: | 92.41 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | NSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVIGVP--EERQRGRKLFE |
| NSR.....E.I..LD...................NENS.R..WDNIK..NIH.IGVP..EE...G..... | |
| Retrocopy | NSRADDTKE*ISELDXXXXXXXXXXXXXXXXXXXNENSIRDFWDNIKHSNIHLIGVPEGEEEDKGAEKLF |
| Parental | E-IIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAARERQQVTYKGKPIR |
| E.IIAE.FPN..KETD.QVQEAQRVPNK..PKRPT.RHIIIKM..IK.KERILKAARE.QQ.TYKG..IR | |
| Retrocopy | E<IIAENFPNQEKETDIQVQEAQRVPNKRNPKRPTPRHIIIKM*RIKVKERILKAAREKQQITYKGNSIR |
| Parental | LSVDFSAKTLQVRREWHDIFK-VKEKNLQPRILYPAR-LSFTMEGEIKSFQDKQKLKEFITKKPILQEML |
| LS.DFSAKT.Q.RRE...I....K.KNLQPRI..P...LSF.ME...K.....QKLK.FIT.K..L..ML | |
| Retrocopy | LSADFSAKTSQARREARYIQS>LKGKNLQPRI--PSK>LSFRMERD-KELSK*QKLKGFITTKLVL*AML |
| Parental | KG |
| KG | |
| Retrocopy | KG |
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_528 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_528 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_528 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,
|