RetrogeneDB ID: | retro_cpor_725 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_25:1670165..1670908(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GPKOW | ||
| Ensembl ID: | ENSCPOG00000013270 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_725
GTACTGTCCCAGACTGTGATGCAGTTCTATGAGGAATCCAAGATGTCTCTAGAGGAAGGAAATAATGCAAGTGTTGATCC
CAGGCACACTATCTTCATGATTCAGAAAGGATGCATACCTCAATGGAAAAAAAGTGAACAGTGAGCCCTGGCTGAGCCAG
AGCCAGAGGTTGATTATGAGGCAGTCCCTGTGGAACCCTATGGGTTGGCCATGATGCAGGGCATGGGCTGGAAACCTGGA
AAGATCATTGGCTGAACTTTTCAATCAAGTGGGCAAGCCCAGTGTAAACTCTAAAGCCCCCAAGGGGTTAGGAATGGGTG
CCAACCTGACCAAAGCCCAGGCATTTGCTTTCATTGCCTGCTGCTTCCTACCAAAGCCAGATGGGGAGCAAGAGAATGAT
AAGGAAGACCAAACTGAAGGGGCTGCTGCCTGGAGGCACTGTGGTGGTTCTTTCTGGCCCTCATCAACACCTCTATTGGA
AGCGAGAAGGCCTTGATCCTGACAATGTACAGGTCGTGGATCATCTAGCAATGGGCTATCACATACCAACTGTTAGCAAC
CTGTGACCTGTACCCCAGCAGAAGTTTGACAAGAATTTCTTGCACCCAGTCCAGGTCCAGATGAGCAGAACTTGCTCTCT
ACAACACATTGGAACAGCTTTATTATGGAAGGCACTCCAAAGTGAAAACTTGCATGGCCAGCAGGAGAACACAGAGAGGA
AATGGAAACACCCTCTAGATAAG
ORF - retro_cpor_725 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.94 % |
| Parental protein coverage: | 51.98 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VLSQAVKELIEESKKSLEERENAGVDPSLAIPMIQKGCIPGEEGADSTPRAETVPEEADYEAVPVEAYGL |
| VLSQ.V....EESK.SLEE..NA.VDP...I.MIQKGCIP..........AE..PE..DYEAVPVE.YGL | |
| Retrocopy | VLSQTVMQFYEESKMSLEEGNNASVDPRHTIFMIQKGCIPQWKKSEQ*ALAEPEPE-VDYEAVPVEPYGL |
| Parental | AMLRGMGWKPGEGIGRTF-NQVVKPRVNLLRPKGLGLGASLTEAQALPSSGSYCPPKPGGEQKKGKEDQP |
| AM..GMGWKPG..IG.TF.NQV.KP.VN...PKGLG.GA.LT.AQA.........PKP.GEQ...KEDQ. | |
| Retrocopy | AMMQGMGWKPGKIIG*TF>NQVGKPSVNSKAPKGLGMGANLTKAQAFAFIACCFLPKPDGEQENDKEDQT |
| Parental | QG-LVPGRTVVVLSGPHRGLYGKVEGLDPDNVRAMVRLALGSRMVTVSEYCLRPVSQQEFDKNLHSDKIG |
| .G.L.PG.TVVVLSGPH..LY.K.EGLDPDNV.....LA.G....TVS...L.PV.QQ.FDKN....... | |
| Retrocopy | EG>LLPGGTVVVLSGPHQHLYWKREGLDPDNVQVVDHLAMGYHIPTVSN--L*PVPQQKFDKNFLHPVQV |
| Parental | QASRTSLGQHNGSSLSRKAHQSEDLRGRQEDPEKKRKHPPDR |
| Q.SRT...QH.G..L..KA.QSE.L.G.QE..E.K.KHP.D. | |
| Retrocopy | QMSRTCSLQHIGTALLWKALQSENLHGQQENTERKWKHPLDK |
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 | 29 .97 RPM |
| SRP017611_kidney | 0 .00 RPM | 25 .02 RPM |
| SRP017611_liver | 0 .00 RPM | 17 .89 RPM |
| SRP040447_lung | 0 .00 RPM | 30 .29 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 12 .46 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_725 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_725 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000013270 | 2 retrocopies |
retro_cpor_148, retro_cpor_725 ,
|
| Felis catus | ENSFCAG00000003818 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000031148 | 1 retrocopy |