RetrogeneDB ID: | retro_pabe_777 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 11:76275949..76276324(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARL6IP1 | ||
| Ensembl ID: | ENSPPYG00000007140 | ||
| Aliases: | ARL6IP1, ARL6IP | ||
| Description: | ADP-ribosylation factor-like protein 6-interacting protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R454] |
Retrocopy-Parental alignment summary:
>retro_pabe_777
TTGGCTGACTACCTTGTTCCCATTCAGGTGCCTAGAATTTTTGGCTCCAATAAATGGACCACTGAACAACAGCAAAGATT
CCATGAAACTTGCAGTAATCTAGTAAAAACTCAAAGCAGAACTGTGGGTTGGTGGAAATGCCTCTTCACACTAAAGGAAG
AAAAACCTAAGCTGTACTTCATGACCATGATCGTTTCCCTTGCCAAGTTTGCTTAGGTGGGACAGCAAGTCCACAACCTG
CTTCTCACCTACCTGATAGTGACTTCCTTACTGTTGCTTCCTGAGCTAAACCAACATGGAATCATTTTGAAGTACATTGG
AGTGGCCAAAAGGGAGCTAACCAAACTTCTCAAACAAAAAGAACAGAAAAATGAA
ORF - retro_pabe_777 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.4 % |
| Parental protein coverage: | 61.58 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LADYLVPILAPRIFGSNKWTTEQQQRFHEICSNLVKTRRRAVGWWKRLFTLKEEKPKMYFMTMIVSLAAV |
| LADYLVPI..PRIFGSNKWTTEQQQRFHE.CSNLVKT..R.VGWWK.LFTLKEEKPK.YFMTMIVSLA.. | |
| Retrocopy | LADYLVPIQVPRIFGSNKWTTEQQQRFHETCSNLVKTQSRTVGWWKCLFTLKEEKPKLYFMTMIVSLAKF |
| Parental | AWVGQQVHNLLLTYLIVTSLLLLPGLNQHGIISKYIGMAKREINKLLKQKEKKNE |
| A.VGQQVHNLLLTYLIVTSLLLLP.LNQHGII.KYIG.AKRE..KLLKQKE.KNE | |
| Retrocopy | A*VGQQVHNLLLTYLIVTSLLLLPELNQHGIILKYIGVAKRELTKLLKQKEQKNE |
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 | 119 .04 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 92 .66 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .25 RPM |
| SRP007412_kidney | 0 .00 RPM | 52 .54 RPM |
| SRP007412_liver | 0 .00 RPM | 60 .47 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_777 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_777 was not experimentally validated.