RetrogeneDB ID: | retro_ecab_1106 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:41758959..41759316(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMA5 | ||
| Ensembl ID: | ENSECAG00000011835 | ||
| Aliases: | None | ||
| Description: | proteasome (prosome, macropain) subunit, alpha type, 5 [Source:HGNC Symbol;Acc:9534] |
Retrocopy-Parental alignment summary:
>retro_ecab_1106
AATCTTCTCTCATTGTTTCCAAGATTATTTCATGAGTAATATGTCATTGGGATGATCAAGCTTTGTTCCATAGCGATTGG
GATACAGACTTCAGAGGTGTGTGTGCCTAGCTATAAAGAAGAGAATTACCTCCTATTGCCCTGTAGCAGTGAGAAAGTTG
TAGATATTGATGCTCAAACAAGTTGTGTTGAAAGTAACCTAATGGCTGGAGCTAAGACTATAATTGATAAAGCCAGAGTG
GAGACATCGGACCTCTGCTTCACTTACAAAAAGATAAATGATATTGAAGAATAAAGCTAGTTTGAGTCCAACTTGAATGT
GCAATTTGGAGAAGAAAATACAGATCCAGAAGCCATT
ORF - retro_ecab_1106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.41 % |
| Parental protein coverage: | 50.21 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLI |
| N..S...RLF...Y.I..IKL.S.AIGIQTSE.VC....K.....L..P.S.EK.V.IDA...C..S.L. | |
| Retrocopy | NLLSLFPRLFHE*YVIGMIKLCSIAIGIQTSE-VCVPSYKE-ENYLLLPCSSEKVVDIDAQTSCVESNLM |
| Parental | ADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAM |
| A.AKT.IDKARVET....FTY......E......SNL..QFGEE..DP.A. | |
| Retrocopy | AGAKTIIDKARVETSDLCFTYKKINDIEE*S*FESNLNVQFGEENTDPEAI |
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 | 10 .68 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 20 .67 RPM |
| SRP021940_embryo | 0 .00 RPM | 28 .10 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 28 .82 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 18 .50 RPM |
| SRP021940_testis | 0 .00 RPM | 34 .02 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1106 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1106 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1106 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000013670 | 1 retrocopy | |
| Equus caballus | ENSECAG00000011835 | 1 retrocopy |
retro_ecab_1106 ,
|
| Echinops telfairi | ENSETEG00000012916 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000068749 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000008863 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000019868 | 2 retrocopies | |
| Sus scrofa | ENSSSCG00000006830 | 2 retrocopies |