RetrogeneDB ID: | retro_ptro_179 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 1:104993620..104994071(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | THAP3 | ||
| Ensembl ID: | ENSPTRG00000000093 | ||
| Aliases: | None | ||
| Description: | THAP domain containing, apoptosis associated protein 3 [Source:UniProtKB/TrEMBL;Acc:K7AUB3] |
Retrocopy-Parental alignment summary:
>retro_ptro_179
CAGGTGAGGGAGAACACACACACTGCCAGTGAGAGAGGAAATGCCAGCTCTTTTCAGAAAGAAAAGGTCCTCCCTGAGGC
GGGGGCTGGAGAGGACAGCCCTGGGAGAAACATGGACACTGCGCTTGAAGAGCTTCAATTGCCCCCAAATGCCAAAGGCC
CCGTAAAACAGATCTCGCCACGGAGGCCGCAAGCAGCAGAGACTGTTGGCCGGCCGGCCGGCCCTGCAGGCTTGAGAAGG
CCCCCCGACAAGCAGCCATCTGATCACAGCTATGCCCTTTTGGACTTAGATTCCCTGAAGAAAAAAACTCTTCCTCACTC
TGAAGGAAAATGAAAAGCTCCAGAAGCGCTTGCAGGCCCAGAGGCTGGTGAAGTGAAGGATGTCCAGCTGCCTCCGTGCC
TGCAAAGGGCACCGGGGACTCCAGGCCAGACTTGGGCCAGAGCAGCAGAGC
ORF - retro_ptro_179 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.74 % |
| Parental protein coverage: | 62.76 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QVRENTDPANERGNASSSQKEKVLPEAGAGEDSPGRNMDTALEELQLPPNAEGHVKQVSPRRPQATEAVG |
| QVRENT..A.ERGNASS.QKEKVLPEAGAGEDSPGRNMDTALEELQLPPNA.G.VKQ.SPRRPQA.E.VG | |
| Retrocopy | QVRENTHTASERGNASSFQKEKVLPEAGAGEDSPGRNMDTALEELQLPPNAKGPVKQISPRRPQAAETVG |
| Parental | RPTGPAGLRRPPSKQPSDHSYALLDLDSLK-KKLFLTLKENEKLRKRLQAQRLVMRRMSSRLRACKGHQG |
| RP.GPAGLRRPP.KQPSDHSYALLDLDSLK.KKLFLTLKENEKL.KRLQAQRLV..RMSS.LRACKGH.G | |
| Retrocopy | RPAGPAGLRRPPDKQPSDHSYALLDLDSLK>KKLFLTLKENEKLQKRLQAQRLVK*RMSSCLRACKGHRG |
| Parental | LQARLGPEQQS |
| LQARLGPEQQS | |
| Retrocopy | LQARLGPEQQS |
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 .02 RPM | 13 .87 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 9 .54 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .91 RPM |
| SRP007412_kidney | 0 .00 RPM | 10 .46 RPM |
| SRP007412_liver | 0 .07 RPM | 4 .98 RPM |
| SRP007412_testis | 0 .63 RPM | 3 .79 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_179 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_179 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_179 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000041988 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000008620 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000001935 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000000093 | 1 retrocopy |
retro_ptro_179 ,
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