RetrogeneDB ID: | retro_ptro_3313 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | Y:26200030..26200406(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNASEH2C | ||
| Ensembl ID: | ENSPTRG00000038742 | ||
| Aliases: | None | ||
| Description: | Ribonuclease H2, subunit C [Source:UniProtKB/TrEMBL;Acc:K6ZY76] |
Retrocopy-Parental alignment summary:
>retro_ptro_3313
CCCACCACGGTGCGGCGCTTCATCACGCCTGCCATCCGCCAGGGCCCCGAGGGACTCTTAAGTGTAGTTTCGGGGCCGCA
GTCTACGGGGCGACGAGGTGGCAGTGCCGTCCGGCCTCGTGGGATACGTGATGGTGACTGAACAGGAGGAGGTGTCGATG
GGGAAGCCAAACCCCTGGCGGGGTTCCGGGAGTGACAACCAAGAAGAGGAGCTTCTGGAGCGGGACTTTGACCGCTTCCT
CGGAACCACTACCAGCTTCAGCCGCTTCACCCTGTAGGGCACCCTGTGGGGCTTCCTTGGCCCGGAAGCCAAACTGCGTG
GGGCCTTAACTTGGCCCAGCCTCGCGGCAACGATTCACGCGCAGGTGCCCAAGGAC
ORF - retro_ptro_3313 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.6 % |
| Parental protein coverage: | 89.21 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PAPVGRFFTPAIRQGPEGLE-VSFRGRCLRGEEVAVPPGLVGYVMVTEEKEVSMGKPDPLRDSGTDDQEE |
| P..V.RF.TPAIRQGPEGL..V.FRGR.LRG.EVAVP.GLVGYVMVTE..EVSMGKP.P.R.SG.D.QEE | |
| Retrocopy | PTTVRRFITPAIRQGPEGLL>V*FRGRSLRGDEVAVPSGLVGYVMVTEQEEVSMGKPNPWRGSGSDNQEE |
| Parental | EPLERDFDRFIGATANFSRFTLWG-LETIPGPDAKVRGALTWPSLAAAIHAQVPED |
| E.LERDFDRF.G.T..FSRFTL.G.L....GP.AK.RGALTWPSLAA.IHAQVP.D | |
| Retrocopy | ELLERDFDRFLGTTTSFSRFTL*GTLWGFLGPEAKLRGALTWPSLAATIHAQVPKD |
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 .02 RPM | 11 .31 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .54 RPM |
| SRP007412_heart | 0 .03 RPM | 7 .26 RPM |
| SRP007412_kidney | 0 .00 RPM | 16 .66 RPM |
| SRP007412_liver | 0 .03 RPM | 12 .01 RPM |
| SRP007412_testis | 0 .00 RPM | 9 .48 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3313 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3313 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_3313 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000019837 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000038742 | 1 retrocopy |
retro_ptro_3313 ,
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