RetrogeneDB ID:

retro_opri_1053

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_6289:121938..122343(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A1
Ensembl ID:ENSOPRG00000011649
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]


Retrocopy-Parental alignment summary:






>retro_opri_1053
AGAGGACGATACCATGGGCTCACGACCACCGTGCTGAAGCAGGGCTCCAGCCAGGGCCATCCGCTTCTTCGTCATGACTT
CCCTGCGCAAGCTGGTACCGAAGCGACAACCCCAACAAGCCCATGAACCCGCTCATCACTGGGGTCTTTGGGGCCATCGC
GGGAGCTGCCAGTGTCTTTGGGAACACCCCACTGGATGTGATCAAGACCCCGGATGCAGGGGCTAGAGGCACACAAGTAC
CGCAACACGTACGACTGCGGCTTGCAGATCTTGAGGAAGGAGGGACTCAAGGCGTTCTACAAGGGCACGGTCCCCCGCCT
GGGCCGCGTGTGCCTGGACGTGGCCATCGTGTTCATCATCTACGACGAGGTGGTGAAGCTGCTGAACAAGGTGTGGAAGA
CGGAC

ORF - retro_opri_1053 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.97 %
Parental protein coverage: 85.35 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKGTYQGLTATVLKQGSNQ-AIRFFVMTSLR-NWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIK
.G.Y.GLT.TVLKQGS.Q.AIRFFVMTSLR..WYR.DNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIK
RetrocopyRGRYHGLTTTVLKQGSSQ>AIRFFVMTSLR>SWYRSDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIK
ParentalT-RMQGLEAHKYRNTWDCGLQILRKEGLKAFYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD
T.RMQGLEAHKYRNT.DCGLQILRKEGLKAFYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD
RetrocopyT>RMQGLEAHKYRNTYDCGLQILRKEGLKAFYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD

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_1053 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 8 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001000752 retrocopies
Gorilla gorilla ENSGGOG000000061982 retrocopies
Macaca mulatta ENSMMUG000000054314 retrocopies
Nomascus leucogenys ENSNLEG000000052152 retrocopies
Ochotona princeps ENSOPRG00000011649 1 retrocopy
retro_opri_1053 ,
Pongo abelii ENSPPYG000000297859 retrocopies
Pan troglodytes ENSPTRG000000140573 retrocopies
Tursiops truncatus ENSTTRG000000068451 retrocopy



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