RetrogeneDB ID: | retro_pabe_2979 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 6:92880903..92881277(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RHOC | ||
| Ensembl ID: | ENSPPYG00000010686 | ||
| Aliases: | None | ||
| Description: | ras homolog family member C [Source:HGNC Symbol;Acc:669] |
Retrocopy-Parental alignment summary:
>retro_pabe_2979
GTCCGTGTCGGTGACGGAGTCTGTGGCAAGACATGCTTGCTCATTGTCTTCAGCAAGGACCAGTTCCCAGAGGGGTGCGC
ACCCTCAGGGTTTCAGAACTATGTGGCCCATATTGAGGATGGGAAACGCGTAGAGCTGACTTTGTGGGACACAGCCAGGC
AGGAAGATTAGGATCGCCTGAGGTCCCTCTTTTACTCAGACACTGATGTTATGTGTTCTCCGTTGACAATCCTGATAGTC
TAGAAAACATCTCAGAGAAATGGAGCCCAGAAGTCAAGCATTTCTGTCCCAACGTGCCCACCGGCCTGGTTGGGAACAAG
AAGGATCTTCGGAATGATGTGCACACAAGGTGGGAGCTAGCCAAGATGAAGCAG
ORF - retro_pabe_2979 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.74 % |
| Parental protein coverage: | 75.74 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTD |
| V.VGDG.CGKTCLLIVFSKDQFPE...P..F.NY.A.IE.DGK.VEL.LWDTA.QED.DRLR.L.Y.DTD | |
| Retrocopy | VRVGDGVCGKTCLLIVFSKDQFPEGCAPSGFQNYVAHIE-DGKRVELTLWDTARQED*DRLRSLFYSDTD |
| Parental | VILMC-FSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQ |
| V..MC.FS.D.PDSLENI.EKW.PEVKHFCPNVP..LVGNKKDLR.D.HTR.ELAKMKQ | |
| Retrocopy | V--MC<FSVDNPDSLENISEKWSPEVKHFCPNVPTGLVGNKKDLRNDVHTRWELAKMKQ |
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 | 6 .69 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .19 RPM |
| SRP007412_heart | 0 .00 RPM | 6 .62 RPM |
| SRP007412_kidney | 0 .00 RPM | 23 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 12 .73 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2979 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2979 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2979 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3632 |
| Pan troglodytes | retro_ptro_2456 |
| Gorilla gorilla | retro_ggor_2450 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000004807 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000010686 | 2 retrocopies |
retro_pabe_2013, retro_pabe_2979 ,
|
| Tetraodon nigroviridis | ENSTNIG00000015041 | 1 retrocopy |