RetrogeneDB ID: | retro_cpor_734 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_26:862582..863191(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | OSGEP | ||
| Ensembl ID: | ENSCPOG00000014460 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_734
CTTCTGGCCTATTTTGCAAGCAGAACCAAGATTGGCGTGGGAGTTCTGAAGGATGGTGAGGTTCTGACAAACCCACTGAA
AACCCATGCTACACCTCCAGGCATAGGATTCCTCCCAAGTACTACTGCTAGGCACCACGGAACTATTATCCTAGGATTGC
GGCAGGAAGAACTAACAGAAGCCAGATTAACTTCCCAAGATATCAATTGCATTGCTTACACCAAAGGCCCTAGCATGGGT
ACCCACTGGCTTCCATAGCAGTTGTGGCCCATATGGTGGCTCCGCTGTGGAATAAACCTCTGGAAGCTGTGAACCACTGT
ATAGACCACATTAAAATGGGCGGCCTCATCACTGGGGCCACCAGCCAACTGTAGTATAAGTCAGCAGAGGAAATACTCAG
GTCATTACCTACTCAGAACATCAGTACTGAATCTTTGGGGAAATCATTGATACTGCTGTGGTAATTCTCTGATCACTTTG
TTTGAGTGCTAAAGATTTCCAATGATCCAAGTCCAGGTTACAACGTTACAACAGATGGCAAAACGAGGCTGGAAGCTAGT
TGAGCTGCCATACATTGTAAAGGGGATGGATGTCTCATTTTCAGGGATT
ORF - retro_cpor_734 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.77 % |
| Parental protein coverage: | 63.35 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | VLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGATARHHRAVILDLLQEALTEAGLTSQDIDC |
| .L....S..KIGVGV..DG.VL.NP..T..TPPG.GFLP..TARHH...IL.L.QE.LTEA.LTSQDI.C | |
| Retrocopy | LLAYFASRTKIGVGVLKDGEVLTNPLKTHATPPGIGFLPSTTARHHGTIILGLRQEELTEARLTSQDINC |
| Parental | IAYTKGPGMGA-PLASVAVVARTVAQLWNKPLVGVNHCIGHIEMGRLITGATS-PTVLYVSGGNTQVIAY |
| IAYTKGP.MG..PLAS.AVVA..VA.LWNKPL..VNHCI.HI.MG.LITGATS.PTV..VS.GNTQVI.Y | |
| Retrocopy | IAYTKGPSMGT<PLASIAVVAHMVAPLWNKPLEAVNHCIDHIKMGGLITGATS<PTVV*VSRGNTQVITY |
| Parental | SEHRYRIFGETIDIAV-GNCL-DRFARVLKISNDPSPGYNI-EQMAKCGKKLVELPYTVKGMDVSFSGI |
| SEH.Y.IFGE.ID.AV.GN.L.D.F..VLKISNDPSPGYN...QMAK.G.KLVELPY.VKGMDVSFSGI | |
| Retrocopy | SEHQY*IFGEIIDTAV<GNSL<DHFV*VLKISNDPSPGYNV>QQMAKRGWKLVELPYIVKGMDVSFSGI |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 8 .68 RPM |
| SRP017611_kidney | 0 .00 RPM | 15 .07 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .57 RPM |
| SRP040447_lung | 0 .00 RPM | 19 .80 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 7 .67 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_734 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_734 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000014460 | 1 retrocopy |
retro_cpor_734 ,
|
| Mus musculus | ENSMUSG00000006289 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000005020 | 1 retrocopy |