RetrogeneDB ID: | retro_cpor_180 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_1:51448578..51448888(+) | ||
| Located in intron of: | ENSCPOG00000014936 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AIF1 | ||
| Ensembl ID: | ENSCPOG00000002068 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_180
GCTATGAGCCCAAACAAGGATTCACAGAGAGGAAAAGCTTTCGGACTGCTGAAGGCACAGCAAGAAGGGAGATTGGAGGA
GATCAACAAGCAATTCCTGGATGATCCCAAATACAACCGTGATGAGGACCTGCCCTCCAAACTGGAAGCCTTCAAGAAGA
AATACATGGATTTGACCTGAATGGAAATGGAGACAATGATGTCATGTTCTTGAAGAGAATGCTACTGAAACTTAGGGCCC
TCAAGACCCACTCAAGCTAAAGAAATTAACTGGAGAGGCATCTGGTGGCTCAGCTGCCCTGACTTTCTCA
ORF - retro_cpor_180 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.42 % |
| Parental protein coverage: | 69.59 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AMSQTRDFQGGKAFGLLKAQQEERLEEINKQFLDDPKYSTDEDLPSKLEAYKKKYME-FDLNGNGDIDIM |
| AMS...D.Q.GKAFGLLKAQQE.RLEEINKQFLDDPKY..DEDLPSKLEA.KKKYM..FDLNGNGD.D.M | |
| Retrocopy | AMSPNKDSQRGKAFGLLKAQQEGRLEEINKQFLDDPKYNRDEDLPSKLEAFKKKYMD<FDLNGNGDNDVM |
| Parental | SLKRMLEKLGVPKTH-LELKKLIGEVSGGSGE-TFS |
| .LKRML.KL...KTH.L.LKKL.GE.SGGS...TFS | |
| Retrocopy | FLKRMLLKLRALKTH<LKLKKLTGEASGGSAALTFS |
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 | 7 .53 RPM |
| SRP017611_kidney | 0 .00 RPM | 18 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 21 .46 RPM |
| SRP040447_lung | 0 .00 RPM | 24 .94 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .87 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_180 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_180 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000002068 | 2 retrocopies |
retro_cpor_180 , retro_cpor_532,
|