RetrogeneDB ID: | retro_cpor_1090 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_45:4217278..4217512(-) | ||
| Located in intron of: | ENSCPOG00000010269 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TGIF2-C20orf24 | ||
| Ensembl ID: | ENSCPOG00000011435 | ||
| Aliases: | None | ||
| Description: | TGIF2-C20orf24 readthrough [Source:HGNC Symbol;Acc:44664] |
Retrocopy-Parental alignment summary:
>retro_cpor_1090
ATCATCGCTGTGGTCCTGGATGCCATTTGGGGAGTTTTGCCACTGCAAAATTTCTTGGGAACAGCAGGATTCTGCCTGAT
CAATGCAGGAGTCCTGTACCTCCACTTCAGCAACTATCTACAGATTGATCAGGAAGAATATGGTTGCATGTGGAAACTCA
CAGAAGGATTTATGACTTCTTGTGCTTTGTTCATGGTCATCTGGATCATCTTTCACACTGCCATCCACTATGAC
ORF - retro_cpor_1090 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.54 % |
| Parental protein coverage: | 61.24 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | IIAVVLGVIWGVLPLRGFLGIAGFCLINAGVLYLYFSNYLQIDEEEYGGTWELTKEGFMTSFALFMVIWI |
| IIAVVL..IWGVLPL..FLG.AGFCLINAGVLYL.FSNYLQID.EEYG..W.LT.EGFMTS.ALFMVIWI | |
| Retrocopy | IIAVVLDAIWGVLPLQNFLGTAGFCLINAGVLYLHFSNYLQIDQEEYGCMWKLT-EGFMTSCALFMVIWI |
| Parental | IFYTAIHYD |
| IF.TAIHYD | |
| Retrocopy | IFHTAIHYD |
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 | 13 .52 RPM |
| SRP017611_kidney | 0 .00 RPM | 35 .49 RPM |
| SRP017611_liver | 0 .00 RPM | 51 .41 RPM |
| SRP040447_lung | 0 .00 RPM | 24 .39 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 13 .64 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1090 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1090 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 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000021805 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000011435 | 2 retrocopies |
retro_cpor_1090 , retro_cpor_1382,
|
| Mustela putorius furo | ENSMPUG00000017777 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000000891 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000020317 | 1 retrocopy |