RetrogeneDB ID: | retro_ptro_2397 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 6:145879249..145879811(+) | ||
| Located in intron of: | ENSPTRG00000018680 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RHBDD1 | ||
| Ensembl ID: | ENSPTRG00000012990 | ||
| Aliases: | None | ||
| Description: | rhomboid domain containing 1 [Source:HGNC Symbol;Acc:23081] |
Retrocopy-Parental alignment summary:
>retro_ptro_2397
TTTCTGGATGAACCTGGCTTTGGAAGGTACTGTGCTGTAGGTTTTTCCAGGAGTTTTGTTTGCTTTGGAGTTTCTTAACA
ACCATCATTGCCTTAGAGGCTTTGTCAACATTTTGGGCTTCCTTGTCCTCAACAGATTTGCTTGTTGGGCCACACTTGTG
CCTTTTCACTTATTCTCACCAGGGACTTCCTTCACTGGGCATCTGGCTGGGATTCTTGTTGCATTAATGCACACTCAAGG
GCCTCTGAAGAACATCATGGAAGCATGTGCTGGCATTTTTTTCCCTCCAATTATTGGTTATCCAGGACAGTGATATTACT
TCAATTGTTCAGGCTAGTCTGGATATCAGGATCATTATCTTTATGGCAGGCCAGGTTATTATGAAGAAGCACCCAGGAGC
TATGATATATACACAGCAGTATGGAGAGAAAAAGAACAGCTGGTGAGAGCATGAAGAGCCAGCCCCTGGGATCAAGAAAA
TACCAGGAATAGCTCACTGCCCTGCGGGCTTCTTCTCTCAGAAGAAATGAGACTATAATGGCTTCACAGGTTTGATAGCC
AG
ORF - retro_ptro_2397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.84 % |
| Parental protein coverage: | 59.37 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FMDEPDFKRSCAVGFS-GVLFALKVLNNHYCPGGFVNILGFPVPNRFACWVELVAIHLFSPGTSFAGHLA |
| F.DEP.F.R.CAVGFS.GVLFAL..LNNH.C..GFVNILGF.V.NRFACW..LV..HLFSPGTSF.GHLA | |
| Retrocopy | FLDEPGFGRYCAVGFS>GVLFALEFLNNHHCLRGFVNILGFLVLNRFACWATLVPFHLFSPGTSFTGHLA |
| Parental | GILVGLMYTQGPLKKIMEACAG-GFSSSAGYPGRQYYFNSSGSSGYQDYYPHGRPDHYEEAPGNYDTYTA |
| GILV.LM.TQGPLK.IMEACAG..F....GYPG..YYFN.SG.SGYQD.Y..GRP..YEEAP..YD.YTA | |
| Retrocopy | GILVALMHTQGPLKNIMEACAGIFFPPIIGYPGQ*YYFNCSG*SGYQDHYLYGRPGYYEEAPRSYDIYTA |
| Parental | GLSEEEQLERALQASLWDRGNTRNSPPPYGFHLSPEEMRRQRLHRFDSQ |
| ...E.EQL.RA..AS.WD..NTRNS..P.G..LS.EEMR...LHRFDSQ | |
| Retrocopy | VWREKEQLVRA*RASPWDQENTRNSSLPCGLLLS-EEMRL*WLHRFDSQ |
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 | 4 .52 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .34 RPM |
| SRP007412_heart | 0 .09 RPM | 8 .63 RPM |
| SRP007412_kidney | 0 .00 RPM | 16 .34 RPM |
| SRP007412_liver | 0 .00 RPM | 15 .35 RPM |
| SRP007412_testis | 0 .00 RPM | 44 .58 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2397 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2397 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2397 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3529 |
| Gorilla gorilla | retro_ggor_2386 |
| Pongo abelii | retro_pabe_2915 |
| Callithrix jacchus | retro_cjac_2386 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012767 | 1 retrocopy | |
| Homo sapiens | ENSG00000144468 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000000723 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000013235 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000012990 | 1 retrocopy |
retro_ptro_2397 ,
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