RetrogeneDB ID: | retro_pabe_3574 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | Un:13319482..13320061(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB19 | ||
| Ensembl ID: | ENSPPYG00000018056 | ||
| Aliases: | None | ||
| Description: | RAB19, member RAS oncogene family [Source:HGNC Symbol;Acc:19982] |
Retrocopy-Parental alignment summary:
>retro_pabe_3574
GACGAGCAGTACGATTTCCTCTTCAAGCTGGTGCTGGTGGGCGACGCAAGCGTGGGCAAGACGTGCATGGTGCAGCGCTT
CAAGACCGGCGCCTTCTTGGAGGGCCAGGGAAGCACCATCGGCGTCGACTTCACCATGAAGATGCTGGAGATCCAGGGCA
AGCGGGTCAAGCTGCAGATCTGGGACACGGCCGGCCAGAAGTGGTTCCGCACCATCACCCAGAGATATTACCGCAGTGCC
AATGGGGCCATCCTTGCCTACGACATCACCAAGAGGAGCTCCTTCTTGTCGGTGCCTCACTGGATTGAGGATGTGAGGAA
GTACACGGGTTCCAACATTGTGCAGCTGCTGATCAGGAACAAGTCAGACCTCAGCGAGCTTCGGGAGGTCTCCCTGGCTG
AGGCACAGAGCCTGGCTGAGCACTATGAAATCCTGTGTGCCATTGAGACGTCTGCCAAGGACTCGAGCAAGGTGGAGGAG
GCCTTCCTGAGGGTGGCCACGGAGCTCATCATGCGGCACGGGAGCCCCCTGTTCAGCGAGAAGAGCCCCGACCACATACA
GCTGAACAGCAAGGACATC
ORF - retro_pabe_3574 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.81 % |
| Parental protein coverage: | 88.84 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DENFDYLFKIILIGDSNVGKTCVVQHFKSGVYTETQQNTIGVDFTVRSLDIDGKKVK-QVWDTAGQERFG |
| DE..D.LFK..L.GD..VGKTC.VQ.FK.G...E.Q..TIGVDFT...L.I.GK.VK.Q.WDTAGQ..F. | |
| Retrocopy | DEQYDFLFKLVLVGDASVGKTCMVQRFKTGAFLEGQGSTIGVDFTMKMLEIQGKRVKLQIWDTAGQKWFR |
| Parental | SITQRY-RSAQAAIIAYDITRRSTFESIPHWIHEIEKYGGATVVIILTGNKCDLWEKRHVLFEDACTLAE |
| .ITQRY.RSA..AI.AYDIT.RS.F.S.PHWI....KY.G...V..L..NK.DL.E.R.V....A..LAE | |
| Retrocopy | TITQRYYRSANGAILAYDITKRSSFLSVPHWIEDVRKYTGSNIVQLLIRNKSDLSELREVSLAEAQSLAE |
| Parental | KYGLLAVLETSAKESKNIDEVFVLMAKELIARNSLHLYGESASNGLPLDSSPV |
| .Y..L...ETSAK.S....E.F...A.ELI.R....L..E.......L.S... | |
| Retrocopy | HYEILCAIETSAKDSSKVEEAFLRVATELIMRHGSPLFSEKSPDHIQLNSKDI |
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 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .03 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .10 RPM | 0 .43 RPM |
| SRP007412_liver | 0 .18 RPM | 0 .03 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3574 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3574 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3574 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000000128 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000006573 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000018056 | 1 retrocopy |
retro_pabe_3574 ,
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