RetrogeneDB ID: | retro_ptro_2168 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 5:96476409..96476660(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COX19 | ||
| Ensembl ID: | ENSPTRG00000041621 | ||
| Aliases: | None | ||
| Description: | cytochrome c oxidase assembly homolog 19 (S. cerevisiae) [Source:HGNC Symbol;Acc:28074] |
Retrocopy-Parental alignment summary:
>retro_ptro_2168
ATGTCCACAGCCATAAATCTTAGGACCAAGATCTTCCAGGCATGGCCCCTGGACAAGGGCAGCTTCCCACTGAAACTTTT
CAATAAATATAAAAGCTTAAAGAGAAATTTATGAGGTGCCTTCATGATAATAAATGTAAACATATTTTGCAGAAGAATAA
ATCAAAAGCATATTCAGAATGCAGAATGGAGAGACAACAAAAGGTGTAAAAACCAAGAGGAACACTAGGATTTGGAGATT
TGATAGAAAAT
ORF - retro_ptro_2168 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.59 % |
| Parental protein coverage: | 68.85 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSTAMNFGTKSFQPRPPDKGSFPLDHLGECKSFK-EKFMKCLHNNNFENALCRNESKEYLECRMERSRLG |
| MSTA.N..TK.FQ..P.DKGSFPL......KS.K.EKFM.CLH.N.....L..N.SK.Y.ECRMER.... | |
| Retrocopy | MSTAINLRTKIFQAWPLDKGSFPLKLFNKYKSLK<EKFMRCLHDNKCKHILQKNKSKAYSECRMERQQKV |
| Parental | LLHSGRLHLPELLGN |
| ....G.L....L..N | |
| Retrocopy | *KPRGTLGFGDLIEN |
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 | 135 .15 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 35 .81 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .67 RPM |
| SRP007412_kidney | 0 .00 RPM | 8 .11 RPM |
| SRP007412_liver | 0 .00 RPM | 22 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 2 .53 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2168 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2168 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2168 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3300 |
| Gorilla gorilla | retro_ggor_1312 |
| Macaca mulatta | retro_mmul_2067 |
Parental genes homology:
Parental genes homology involve 7 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000015253 | 1 retrocopy | |
| Homo sapiens | ENSG00000240230 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000034907 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000007202 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000041621 | 1 retrocopy |
retro_ptro_2168 ,
|
| Pteropus vampyrus | ENSPVAG00000002192 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000011489 | 2 retrocopies |