RetrogeneDB ID: | retro_ptro_678 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 12:24826078..24826370(+) | ||
| Located in intron of: | ENSPTRG00000005173 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPS25 | ||
| Ensembl ID: | ENSPTRG00000014658 | ||
| Aliases: | None | ||
| Description: | Pan troglodytes mitochondrial ribosomal protein S25 (MRPS25), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001251923] |
Retrocopy-Parental alignment summary:
>retro_ptro_678
CCTTGGATGCAGATCATGATGTTTAAGAACACAATACCATTACCCTTCCTACAATTCTGTTTATATTATGAAGAGCAGGT
CCTGGTGGATATAGAGATCAAGATGAATAAGGAGATTATGGAACACATCAAAAAAATCGTGGGGAAGAATGAGGACACAA
GAAAGGAGAGCAGGAGAAAAAGCAGCTCTCTCACCCAGCTCATTTTGGCCTTCAAAGTAGTTCTGATGGGAATCTACCTG
TGAAGTTAAAGAGCAGGTGCCCTATCCAGGCCTAATGGCATTAGGAGAAGAC
ORF - retro_ptro_678 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.38 % |
| Parental protein coverage: | 57.23 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PWVQIMMFKNMTPSPFLRFYLDSGEQVLVDVETKSNKEIMEHIRKILGKNEETLRE-EEEEKKQLSHPAN |
| PW.QIMMFKN..P.PFL.F.L...EQVLVD.E.K.NKEIMEHI.KI.GKNE.T..E.E.E.KKQLSHPA. | |
| Retrocopy | PWMQIMMFKNTIPLPFLQFCLYYEEQVLVDIEIKMNKEIMEHIKKIVGKNEDTRKE<EQE-KKQLSHPAH |
| Parental | FG-PRKYCLRECICEVEGQVPCPSLVPLPKE |
| FG.P.K....E..CEV..QVP.P.L..L... | |
| Retrocopy | FG<PSK*F*WESTCEVKEQVPYPGLMALGED |
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_prefrontal_cortex | 0 .00 RPM | 31 .12 RPM |
| SRP007412_cerebellum | 0 .07 RPM | 32 .77 RPM |
| SRP007412_heart | 0 .03 RPM | 36 .58 RPM |
| SRP007412_kidney | 0 .05 RPM | 66 .16 RPM |
| SRP007412_liver | 0 .07 RPM | 40 .16 RPM |
| SRP007412_testis | 0 .42 RPM | 59 .23 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_678 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_678 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_678 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1127 |
| Gorilla gorilla | retro_ggor_880 |
| Pongo abelii | retro_pabe_932 |
| Macaca mulatta | retro_mmul_874 |
| Callithrix jacchus | retro_cjac_3303 |
Parental genes homology:
Parental genes homology involve 11 parental genes, and 12 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017160 | 1 retrocopy | |
| Homo sapiens | ENSG00000131368 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000011005 | 1 retrocopy | |
| Latimeria chalumnae | ENSLACG00000009006 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000005157 | 2 retrocopies | |
| Nomascus leucogenys | ENSNLEG00000005218 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000013409 | 1 retrocopy | |
| Pelodiscus sinensis | ENSPSIG00000008882 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000014658 | 1 retrocopy |
retro_ptro_678 ,
|
| Rattus norvegicus | ENSRNOG00000010912 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000027997 | 1 retrocopy |