RetrogeneDB ID: | retro_cpor_816 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_29:24837927..24838300(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDCD5 | ||
| Ensembl ID: | ENSCPOG00000000159 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_816
ATGGCAGATGTGGAGTTGTAGGCACTGAGACAGCAGTCGCTGGTCGAGCTGCAGACAAAACACAGTGATCCCAAGAATGT
ACCACAGCAGTAAGCAAAGCACAATGAAGCAGAAATGGGAAACAATGTCTTAGCCCAAATTCTGAATCAGTTAGCCAGGG
CCAGATTAAGTCACTTAGCACTTATGAAGTCTGAAAAAACCAAAGAGGTAGACAATTACCTTATACACTTGGCAAGATAT
AAACAGCTAACTGGAATGTCTCAGTACAAGGATTAATAGAAATTCTGGGAAAAGTAAGCTGACAAACAGAAAACAAAAAA
CAGCTAAACTCAACAGAACAAAAGTAATGGACTCTGACAAAGGTGATGGTTAC
ORF - retro_cpor_816 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.89 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MADEELEALRKQRLAELQAKHGFQDPNDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTK |
| MAD.EL.ALR.Q.L.ELQ.KH...DP....QQ.AKH.EAEM.N..LAQ.L.Q.ARARLS.LAL.K.EKTK | |
| Retrocopy | MADVEL*ALRQQSLVELQTKHS--DPKNVPQQ*AKHNEAEMGNNVLAQILNQLARARLSHLALMKSEKTK |
| Parental | AVENYLIQMARYGQLSG-KVSEQGLIEILEKVSQQTE-KKTTVKFNRRKVMDSDEDDDY |
| .V.NYLI..ARY.QL.G..VS.QGLIEIL.KVS.QTE.K..T.K.NR.KVMDSD..D.Y | |
| Retrocopy | EVDNYLIHLARYKQLTG<NVSVQGLIEILGKVS*QTE<KQKTAKLNRTKVMDSDKGDGY |
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 | 15 .82 RPM |
| SRP017611_kidney | 0 .00 RPM | 21 .67 RPM |
| SRP017611_liver | 0 .04 RPM | 18 .80 RPM |
| SRP040447_lung | 0 .00 RPM | 14 .12 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 27 .07 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_816 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_816 was not experimentally validated.