RetrogeneDB ID: | retro_opri_90 | ||
Retrocopy location | Organism: | Southern American pika (Ochotona princeps) | |
| Coordinates: | GeneScaffold_2176:132654..133062(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IMMP2L | ||
| Ensembl ID: | ENSOPRG00000000996 | ||
| Aliases: | None | ||
| Description: | IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae) [Source:HGNC Symbol;Acc:14598] |
Retrocopy-Parental alignment summary:
>retro_opri_90
ATGGCCCAGTCTCAAGGATGGGTGAAAAGATACTGCACGGCCTTTTGCAAAGGCTTCTTCGTGGCAGTGCCCGTGGCAGT
GACTTTGCTGGACCGAGTTGCCTGCGTGGCGAGAGTGGAAGGCACATCAATGCAACCTTCTTTGAATCCTGGGGGGAGCC
GGTCACCTGATGTGGTACTTTTGAACCACTGGAAAGTGAGGAATTTTGAAGTTCAACGTGGTGACATTGTGTCGTTGGTG
TCTCCTAAAAACCCACAGCAGAAAATCATTAAGCGAGTGATTGCTCTTGAAGGAGATATTATCAGAACCATTGGACACAA
AAACCGGTATGTCAGAGTCCCCCGTGGTCACATCTGGGTCGAAGGTGATCACCATGGACACAGTTTTGACAGTAATTCCT
TTGGGCCC
ORF - retro_opri_90 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.12 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAQSQGWVKRYFKAFCKGFFVAVPVAVTVLDRVACVARVEGASMQPCLNPGGSQSSDVVLLNHWKVRNFE |
| MAQSQGWVKRY..AFCKGFFVAVPVAVT.LDRVACVARVEG.SMQP.LNPGGS.S.DVVLLNHWKVRNFE | |
| Retrocopy | MAQSQGWVKRYCTAFCKGFFVAVPVAVTLLDRVACVARVEGTSMQPSLNPGGSRSPDVVLLNHWKVRNFE |
| Parental | VQRGDIVSLVSPKNPQQKIIKRVIALEGDIIRTIGHKNRYVKVPRGHIWVEGDHHGHSFDSNSFGP |
| VQRGDIVSLVSPKNPQQKIIKRVIALEGDIIRTIGHKNRYV.VPRGHIWVEGDHHGHSFDSNSFGP | |
| Retrocopy | VQRGDIVSLVSPKNPQQKIIKRVIALEGDIIRTIGHKNRYVRVPRGHIWVEGDHHGHSFDSNSFGP |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_90 was not experimentally validated.
Retrocopy orthology:
Ochotona princeps 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 | |
|---|---|---|---|
| Ochotona princeps | ENSOPRG00000000996 | 2 retrocopies |
retro_opri_652, retro_opri_90 ,
|