RetrogeneDB ID:

retro_opri_124

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2509:9151..9447(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ISCA2
Ensembl ID:ENSOPRG00000011684
Aliases:None
Description:iron-sulfur cluster assembly 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19857]


Retrocopy-Parental alignment summary:






>retro_opri_124
CTTCTCGCGGCCTCTCCAGGACTTGAGGTGCATCCAGTGGCCTCGTTCTCCGGTGTCGAGGCTGGCAAGGGGCAGATCCA
CCTCATTGACAGCTGTGTCCATAGGCTTCCGAAGATCACCCAAAGGTCAGACTTCCTCTGATTGGAGGAGGAGGTGGGGT
GGAGGCTCCGGATTCCAATACAAGTTTTCACTGGACACGATAATCAACCCCAACGACAGAGTGTTTGAACAGGCGGAGCC
AGAGAAGTGGTGGAATCGAGAGCTTGACCTTGGTGAAAGGCGCCCGGGTGGACTTC

ORF - retro_opri_124 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.51 %
Parental protein coverage: 64.29 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLLAASPGLEARRVASSSGAEAGEGQIHLTDSCVQRLLEITEGSEFLRLEVE-GGGCSGFQYKFSLDTVIN
LLAASPGLE...VAS.SG.EAG.GQIHL.DSCV.RL..IT..S.FL.LE.E..GG.SGFQYKFSLDT.IN
RetrocopyLLAASPGLEVHPVASFSGVEAGKGQIHLIDSCVHRLPKITQRSDFL*LEEE>WGGGSGFQYKFSLDTIIN
ParentalPDDRVFEQ-GGARVVVDS-ESLTFVKGAQVDF
P.DRVFEQ.GGAR.VV.S.ESLT.VKGA.VDF
RetrocopyPNDRVFEQ<GGAREVVES<ESLTLVKGARVDF

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_124 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 9 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000204791 retrocopy
Dipodomys ordii ENSDORG000000148571 retrocopy
Gorilla gorilla ENSGGOG000000128941 retrocopy
Macaca mulatta ENSMMUG000000065661 retrocopy
Nomascus leucogenys ENSNLEG000000162681 retrocopy
Ochotona princeps ENSOPRG00000011684 2 retrocopies
retro_opri_1068, retro_opri_124 ,
Pan troglodytes ENSPTRG000000065361 retrocopy
Rattus norvegicus ENSRNOG000000120851 retrocopy



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