RetrogeneDB ID: | retro_mmul_2343 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 8:57109875..57110326(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMMUG00000000082 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMU.1215 | ||
| Ensembl ID: | ENSMMUG00000011486 | ||
| Aliases: | None | ||
| Description: | signal peptidase complex catalytic subunit SEC11A [Source:RefSeq peptide;Acc:NP_001248505] |
Retrocopy-Parental alignment summary:
>retro_mmul_2343
ATGATTGTCTCATCGGCGCTAATGATCTGGAAGGGGTTAATGGTAATAACTGGGAGTGAAAGTCCAATTGTAGTGCTGCT
CAGTGGCAGCATGGAACCCGCATTTCATAGGGGAGATCTTCTCTTTCTAACAAATCGAGTTGAAGATTCCATACAAGTGG
GAGAAACTGCTGTTTTAAGGATAGAAGGAAGAAGGATTCTTATAGTTCACCGAGTCTTGAAGATTCATGAAAAACAAAAT
GGGCATATCAAGTTTTTGACCAAAGGAGATAATAATGCGGTTGATGACCCAGGCCTCTATAAACAAGAACAACATTCGCT
AGAGAAAAAAGATGTCGTGGGGAGAGCCAGGGGATTTTTCTTGTATTGGAATTGGGACCATCCTCATGAATGACTATCCT
AAATTTAAGTATGAAGTGCTATTTTTGCTGGGTTTATTTGTGATGGTCCAT
ORF - retro_mmul_2343 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.97 % |
| Parental protein coverage: | 98.69 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHRGDLLFLTNRVEDPIRVGEIVVFRIEGREIPIVH |
| MIVSSALMIWKGLMVITGSESPIVV.LSGSMEPAFHRGDLLFLTNRVED.I.VGE..V.RIEGR.I.IVH | |
| Retrocopy | MIVSSALMIWKGLMVITGSESPIVVLLSGSMEPAFHRGDLLFLTNRVEDSIQVGETAVLRIEGRRILIVH |
| Parental | RVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVV-GRARGFV-PYIGIVTILMNDYPKFKY |
| RVLKIHEKQNGHIKFLTKGDNNAVDD.GLYKQ.QH.LEKKDVV.G...G.....IGI.TILMNDYPKFKY | |
| Retrocopy | RVLKIHEKQNGHIKFLTKGDNNAVDDPGLYKQEQHSLEKKDVV<GESQGIF<SCIGIGTILMNDYPKFKY |
| Parental | AVLFLLGLFVLVH |
| .VLFLLGLFV.VH | |
| Retrocopy | EVLFLLGLFVMVH |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 13 .33 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 8 .57 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .14 RPM |
| SRP007412_heart | 0 .00 RPM | 23 .67 RPM |
| SRP007412_kidney | 0 .00 RPM | 28 .17 RPM |
| SRP007412_liver | 0 .00 RPM | 16 .03 RPM |
| SRP007412_testis | 0 .00 RPM | 47 .57 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2343 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2343 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2343 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4058 |
| Pan troglodytes | retro_ptro_2751 |
| Gorilla gorilla | retro_ggor_2726 |
| Pongo abelii | retro_pabe_3333 |
Parental genes homology:
Parental genes homology involve 7 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000015328 | 2 retrocopies | |
| Macaca mulatta | ENSMMUG00000011486 | 1 retrocopy |
retro_mmul_2343 ,
|
| Monodelphis domestica | ENSMODG00000019364 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000008205 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000007281 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000019948 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000012320 | 3 retrocopies |