RetrogeneDB ID: | retro_cpor_1024 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_4:6050279..6050632(-) | ||
| 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_1024
TTGAGGAGGCAGCACCCAGCTGAGCTGCAGGGAAAACACAGGGTTCCTAACGATGCAGCACAATGGGAGGCAAAGCCCTG
GGGAGCAGGGACGAGGAACCATGTCTTAGTCCAAGCTTTGGATCAATCAGCCTGGGCCAGGCTAAGTAATATAGCACCAT
AAACCCTAAAACAAAAGCAATAGAGCATTACATTGTACAGAAGGCAAGATATGGACAACTAACTGGGAAAGTCTCAGAAT
AAAATTTAATAGAAATCCTTGGGGGTGGAGGAATAAGCCAGCAAGCAGAAAAGAACACAGCAGTTAAATTCAGCAGAAGA
AAAGTAACAGACTATGACGAAGGTGACAATTAT
ORF - retro_cpor_1024 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.3 % |
| Parental protein coverage: | 93.7 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LRKQRLAELQAKHGFQDPNDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLA-LVKPEKTKAVENYLI |
| LR.Q..AELQ.KH....PNDAAQ.EAK...A..RN..L.Q.LDQSA.ARLSN.A....P.KTKA.E.Y.. | |
| Retrocopy | LRRQHPAELQGKH--RVPNDAAQWEAKPWGAGTRNHVLVQALDQSAWARLSNIA<TINP-KTKAIEHYIV |
| Parental | QMARYGQLSGKVSEQGLIEIL--EKVSQQTEKKTTVKFNRRKVMDSDEDDDY |
| Q.ARYGQL.GKVSE..LIEIL.....SQQ.EK.T.VKF.RRKV.D.DE.D.Y | |
| Retrocopy | QKARYGQLTGKVSE*NLIEILGGGGISQQAEKNTAVKFSRRKVTDYDEGDNY |
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_1024 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1024 was not experimentally validated.