RetrogeneDB ID: | retro_cpor_311 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_12:42251545..42251976(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCDC152 | ||
| Ensembl ID: | ENSCPOG00000002761 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_311
AGTTCAAGAATGGATCAAAGCAGAAGATGTGCAAAAAGACTAGCAGTGTGAACATTAACAAGAGTTATGAAAGATTTGCC
AAAGATAGAAAAGAAAATGATATAAACCAGTGGAAAGAGTAACAGACTGGAGATTCAGGTGGAAAAGACTTCCCATTTAT
TAAAGATAATCCAAACAAAGAAAACCTCATTTAAAAAAGAATGTGCTGCTCTTCATGATATGATAAAAGTGCTACAACAG
ACTGTCAAATATCAACACAATTGGAAAGGTGAAAATAAACAATTACAAAGAAATGATGATACGACAAAGAAAAGCTAAAA
TCTCAAGAACAAGAATATAAGAATAATATCACCAAACTTATACATGAAGTGAAAATCAAAGAGGAGGAACTTAAGATAGA
AATAAGCAAACTTTATCAAGATATGGAGAAA
ORF - retro_cpor_311 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.44 % |
| Parental protein coverage: | 56.64 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SSSMDQSSNECTKKISNVNIDKLIKDFSQIEKKMIETSGKNNILEIQLEKTTCLLKVIQTKETSFKKECA |
| SS.MDQS...C.K...........KD...IEKKMI.TSGK.N.LEIQ.EKT..LLK.IQTK.TSFKKECA | |
| Retrocopy | SSRMDQS-RRCAKRLAV*TLTRVMKDLPKIEKKMI*TSGKSNRLEIQVEKTSHLLKIIQTKKTSFKKECA |
| Parental | ALHDMIKGLQQTIEYQHNLKGENEELKRNADLA-KEKLKSQEQEHMNNIAKLEYEMKIKEEQHKVEISRL |
| ALHDMIK.LQQT..YQHN.KGEN..L.RN.D...KEKLKSQEQE..NNI.KL..E.KIKEE..K.EIS.L | |
| Retrocopy | ALHDMIKVLQQTVKYQHNWKGENKQLQRNDDTT<KEKLKSQEQEYKNNITKLIHEVKIKEEELKIEISKL |
| Parental | YQDMQK |
| YQDM.K | |
| Retrocopy | YQDMEK |
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 | 2 .76 RPM |
| SRP017611_kidney | 0 .00 RPM | 5 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 20 .37 RPM |
| SRP040447_lung | 0 .00 RPM | 1 .36 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .43 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_311 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_311 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 | ENSCPOG00000002761 | 2 retrocopies |
retro_cpor_311 , retro_cpor_638,
|
| Mustela putorius furo | ENSMPUG00000014443 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000012867 | 1 retrocopy |