RetrogeneDB ID: | retro_pabe_253 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1:70643619..70644219(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SERPINA5 | ||
| Ensembl ID: | ENSPPYG00000006108 | ||
| Aliases: | None | ||
| Description: | serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5 [Source:HGNC Symbol;Acc:8723] |
Retrocopy-Parental alignment summary:
>retro_pabe_253
GCTAAGTGGGAGACAAGCTTCAACCACAAAGGCACCCAAGAGCAGGACTTCTACGTGACCTCGGAGACTGTGGTCCGGGT
ACCCATGATGAGCCGCGAGGATTAGTATCACTACCTCCTGGACCGGAACCTCTCCTGCAGGGTGGTGGGGGTCCCCTACC
AAGGCAATGCCACAGCTTTGTTCATTCTCCCCAGTGAGGGAAAGATGCAGCAGGTGGAGAATGGACTGAGTGAGAAAACG
CTGAGGAAGTGGCTTAAGATATTCAAAAAGAGGCAGCTCGAGCTTTGCCTTCCCAAATTCTCCATTGAGGGCTCCTATCA
GCTGGAGAAAGTCCTCCCCAAGCTGGGGATCAGTAACGTCTTCACCTCCCATGCTGATCTGTCTGGCATCAGCAACCACT
CAAATATCCAGGTGTCTGAGATGGTGCACAAAGCTGTGGTGGAGGTGGATGAGTCGGGAACCAGAGCAGCGGCAGCCACG
GGGACAATCTTCACATTCAGGTCGGCCCACCTGAACTCTCAGAGGATAGTGTTCAACAGGCCCTTTCTGATGTTCATTGT
GGATAACAATATCCTCTTCCTTGGCAAAGTGAACCGCCCC
ORF - retro_pabe_253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.5 % |
| Parental protein coverage: | 53.62 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AKWETSFNHKGTQEQDFYVTSETVVRVPMMSREDQYHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQ |
| AKWETSFNHKGTQEQDFYVTSETVVRVPMMSRED.YHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQ | |
| Retrocopy | AKWETSFNHKGTQEQDFYVTSETVVRVPMMSRED*YHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQ |
| Parental | QVENGLSEKTLRKWLKMFKKRQLELCLPKFSIEGSYQLEKVLPKLGISNVFTSHADLSGISNHSNIQVSE |
| QVENGLSEKTLRKWLK.FKKRQLELCLPKFSIEGSYQLEKVLPKLGISNVFTSHADLSGISNHSNIQVSE | |
| Retrocopy | QVENGLSEKTLRKWLKIFKKRQLELCLPKFSIEGSYQLEKVLPKLGISNVFTSHADLSGISNHSNIQVSE |
| Parental | MVHKAVVEVDESGTRAAAATGTIFTFRSARLNSQRIVFNRPFLMFIVDNNILFLGKVNRP |
| MVHKAVVEVDESGTRAAAATGTIFTFRSA.LNSQRIVFNRPFLMFIVDNNILFLGKVNRP | |
| Retrocopy | MVHKAVVEVDESGTRAAAATGTIFTFRSAHLNSQRIVFNRPFLMFIVDNNILFLGKVNRP |
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 | 0 .66 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .24 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .10 RPM | 36 .26 RPM |
| SRP007412_liver | 1 .59 RPM | 380 .44 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_253 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_253 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_253 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000003691 | 2 retrocopies | |
| Pongo abelii | ENSPPYG00000006108 | 1 retrocopy |
retro_pabe_253 ,
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