RetrogeneDB ID: | retro_cpor_1291 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_65:8175759..8177113(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CEP70 | ||
| Ensembl ID: | ENSCPOG00000008134 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1291
ATCTCTGCCAGCAACAATAAAATGAAAAATCTTCAAAAGGAGAATAGAGTTTTACAGTCAAAATGCCAGAATTACAAGAA
AAAAGAAATAGAACAGCAAATAATGCTTCTTTGCAAAACTATGTCTGTCAACTAAGAAAAGAGGAGAAAGAACAAATTCT
CACTCAAAACATGTTTTCTTACCTGTGCAAAGGAGTTCTTCACATAGTCATGGATTGACAGTTGCTTTGCTTGATTAATT
ATTAAGAATCTAAAATTAGAAAAATCCATGCACCTCTGTGTATAAAAAAGATGAAAGTCAATCAGAAGAATAAAATGATT
ATAAAAATATGACTGCTTCACCACCTCACCAAAGCCTTCTAATGTCATTGCCAAATCAACTCAAGAAGTCGAATTCCAAG
ATTAATGCACTTTTAGTGCATAGCTAAACCTTCCAAAAGATTTAGAAAGCAGGACCTTACAACATGAATAATACTTTATA
AGTGACAAGTGAAGAAACTGGAAAAATTCCTTAATAAAGAATAAAATTACAAGAGCTTATGAGTCATAAAAAACACTGAG
GACACAGAGAAAAAAGTGAACCCAGCAGAGAAAACCATCAACAGGCACTAGTTAAGCAGAGATACTTTCAGGTTCTGTGT
AGCATCAGCTCAACTATTTATAATCTGAGAGCTCCTTGATCATTTATAAACAGAGCAAAGGATCCCAACATTTAACAAAG
ACCTTGTTTAAGACTGTGGATTTGAACATCTTGTTCCTCTAATAGAAATGTGGGCAGGCAAACAGATATCCCTGAAGGAT
TTACATAATTCTGTAAGAATACTATATACAGATCTGATGCCTTGGCATAATTTTAAGAAACAGGATGAAAATGAAGGTGT
CATAGTTGGAAATCTGTTGTTTATGGTGAATTCTATGTTAGAGGAAGTTGAAAATTAGGAAAAGGACAGCAGCATGCCAA
AATTTCAATCTTTGCCAGCTATTGTATCTTACTTTCACAAATTTTTGCTGTACCTTCTCTAAATGGAGTCCATCTTCAAA
TGAATGAAGTTTATAGTAGGCATTGAGAAATGAACAATGCTGTGAGGAACCTCCAAGAACACTTAGAATTAGATAGTTTA
TCTTCATGGTGTGTACTGGTGAGCACAGCTGAAAAACTGTGTAGGCTGATTAATGAGGATGTGACTGAGCAGGGTAAGAA
AGTACCAGGACCTGAAGACCTCAATAGTGTTGTTAACAGATTGGAATAACAGGAGGAATTTTCCCCAGCATTTCAGGTAT
TTATTAGTGATCTACTTGAAATCTTAGAAACTGATGACTAGGATAAAATAAACAATTTAAAAGTACTTTCATAC
ORF - retro_cpor_1291 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.53 % |
| Parental protein coverage: | 80.28 % |
| Number of stop codons detected: | 10 |
| Number of frameshifts detected: | 10 |
Retrocopy - Parental Gene Alignment:
| Parental | VCQQQNQMKDLQKEHRTLQSKCQHYKKKQLEQHQTI-ASLQKDICRLKKEEEERVITQNRVFAYLCKRVP |
| .....N.MK.LQKE.R.LQSKCQ.Y.KK.....Q...ASLQ...C.L.KEE.E...TQN..F.YLCK.V. | |
| Retrocopy | ISASNNKMKNLQKENRVLQSKCQNY-KKKEIEQQIM<ASLQNYVCQLRKEEKEQILTQN-MFSYLCKGVL |
| Parental | HTVLDKQLLCLIDYYESKIRKIFTQ-RQYRKDESQSEEEKDYRNLNVSRPYKGLLMSLQNQLKESNSKID |
| H.V.D.QLLCLI.Y.ESKIRKI......Y.KDESQSEE..DY.N...S.P...LLMSL.NQLK.SNSKI. | |
| Retrocopy | HIVMD*QLLCLINY*ESKIRKIHAP<SVYKKDESQSEE*NDYKNMTASPPHQSLLMSLPNQLKKSNSKIN |
| Parental | ALL-SEKLKLQKDLENRPTQHE-LRLYKQQVKKLEKALKKN-IKLQELISYTK-TEDTEKK-DEANKENQ |
| ALL.S..L.L.KDLE.R..QHE...LYK.QVKKLEK.L.K..IKLQEL.S..K.TEDTEKK..E...EN. | |
| Retrocopy | ALL<SA*LNLPKDLESRTLQHE<IILYK*QVKKLEKFLNKE<IKLQELMSHKK>TEDTEKK<SEPSRENH |
| Parental | QQALIDQRYFQVLCSINSIIHNPRAP-VIIYKQSKESQH-FNKDFVQDYGFEHLVPIIEMWADELTSLKD |
| QQAL..QRYFQVLCSI.S.I.N.RAP..IIYKQSK.SQH.FNKD.V.D.GFEHLVP.IEMWA....SLKD | |
| Retrocopy | QQALVKQRYFQVLCSISSTIYNLRAP<LIIYKQSKGSQH<FNKDLV*DCGFEHLVPLIEMWAGKQISLKD |
| Parental | LYKSLKILSTELVPWHNFKKQDVSEGVRVEDLLFMVDAMLEEAENKKKDSNTPNFQTLQAIVSHFQK-LF |
| L..S..IL.T.L.PWHNFKKQD..EGV.V..LLFMV..MLEE.EN..KDS..P.FQ.L.AIVS.F.K..F | |
| Retrocopy | LHNSVRILYTDLMPWHNFKKQDENEGVIVGNLLFMVNSMLEEVEN*EKDSSMPKFQSLPAIVSYFHK<IF |
| Parental | DVPSLNGVYPRMNEVYSRLGEMNNAVRNLQELLELDSSSSLCVLVSTVGKLCRLINEDVNEQVKQVLGPE |
| .VPSLNGV...MNEVYSR..EMNNAVRNLQE.LELDS.SS.CVLVST..KLCRLINEDV.EQ.K.V.GPE | |
| Retrocopy | AVPSLNGVHLQMNEVYSRH*EMNNAVRNLQEHLELDSLSSWCVLVSTAEKLCRLINEDVTEQGKKVPGPE |
| Parental | DLQSIISRLEEHEEFFPAFQAFANDLLEILEIDDLDAIVPAVKKLKVLSY |
| DL.S...RLE..EEF.PAFQ.F..DLLEILE.DD.D.I......LKVLSY | |
| Retrocopy | DLNSVVNRLE*QEEFSPAFQVFISDLLEILETDD*DKI----NNLKVLSY |
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 | 11 .04 RPM |
| SRP017611_kidney | 0 .00 RPM | 20 .52 RPM |
| SRP017611_liver | 0 .04 RPM | 10 .05 RPM |
| SRP040447_lung | 0 .00 RPM | 9 .99 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 4 .77 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1291 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1291 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000008134 | 1 retrocopy |
retro_cpor_1291 ,
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