RetrogeneDB ID: | retro_ptro_100 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | GL389461.1:5315..6080(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSPTRG00000039510 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB41 | ||
| Ensembl ID: | ENSPTRG00000021994 | ||
| Aliases: | None | ||
| Description: | RAB41, member RAS oncogene family [Source:HGNC Symbol;Acc:18293] |
Retrocopy-Parental alignment summary:
>retro_ptro_100
ATGTCCGCGGGCGGAGACCTCGGGAATCCGCTGAGGAAATTCAAGCTGGTGTTCCTGGGGGAGCAAAGCGTTGCAAAGAC
ATCTTTGATCACCAGATTCATGTATGACAGTTTTGACAACACCTATCAGGCAACAATTGGCATTGACTTTTTATCAAAAA
CTATGTACTTGGAGGATGGAACAATCGGGCTTCGGCTGTGGGATACGGCGGGTCAGGAACGTCTCCGTAGCCTCATTCCC
AGGTACATCCGTGATTCTGCTGCAGCTGTAGTAGTTTACGATATCACAAATGTTAACTCATTCCAGCAAACTACAAAGTG
GATTGATGATGTCAGAACAGAAAGAGGAAGTGATGTTATCATCACGCTAGTAGGAAATAGAACAGATCTTGCTGACAAGA
GGCAAGTGTCAATTGAGGAGGGAGAGAGGAAAGCCAAAGGGCTGAATGTTAGGTTTATTGAAACTAGGGCAAAAGCTGGA
TACAATGTAAAGCAGCTCTTTCGACGTGTAGCAGCAGCTTTGCCGGGAATGGAAAGCACACAGGACAGAAGCAGAGAAGA
CATGAGTGACATAAAACTGGAAAAGCCTCAGGAGCAACCAGTCAGCGAAGGGGGTTGTTCCTGCTACTCTCCCATGTCAT
CTTCAACCCTTCCTCAGAAGCCCCCTTACTCTTTCATTGACTGCAGTGTGAATATTGGCTTGAACCTTTTCCCTTCATTA
ATAACGTTTTGCAATTCATCATTGCTCCCTGTCTCGTGGAGATGA
ORF - retro_ptro_100 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.77 % |
| Parental protein coverage: | 84.16 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LCKSKLLFLGEQSVGKTSIISRFMYNSFGCACQATVGIDFLSKTMYLEDQIVQLQLWDTAGQERFHSLIP |
| L.K.KL.FLGEQSV.KTS.I.RFMY.SF....QAT.GIDFLSKTMYLED....L.LWDTAGQER..SLIP | |
| Retrocopy | LRKFKLVFLGEQSVAKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDGTIGLRLWDTAGQERLRSLIP |
| Parental | SYIRDSTIAVVVYDITNINSFKETDKWVEHV-AERGDDVVIMLLGNKIDFDNKRQVTAEQGEEKSRNLNV |
| .YIRDS..AVVVYDITN.NSF..T.KW...V..ERG.DV.I.L.GN..D...KRQV..E.GE.K...LNV | |
| Retrocopy | RYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIITLVGNRTDLADKRQVSIEEGERKAKGLNV |
| Parental | MFIETSAKTGYNVKKLFRRVASALLSTR-TSPPPKEGTVEIELESFEE |
| .FIET.AK.GYNVK.LFRRVA.AL.....T.....E....I.LE...E | |
| Retrocopy | RFIETRAKAGYNVKQLFRRVAAALPGMESTQDRSREDMSDIKLEKPQE |
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 | 2 .25 RPM | 3 .99 RPM |
| SRP007412_cerebellum | 0 .32 RPM | 2 .29 RPM |
| SRP007412_heart | 0 .03 RPM | 0 .76 RPM |
| SRP007412_kidney | 0 .00 RPM | 1 .31 RPM |
| SRP007412_liver | 0 .13 RPM | 0 .13 RPM |
| SRP007412_testis | 0 .84 RPM | 1 .26 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_100 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_100 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_100 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pan troglodytes | ENSPTRG00000021994 | 1 retrocopy |
retro_ptro_100 ,
|