RetrogeneDB ID:

retro_opri_1094

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_705:199898..200569(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AK4
Ensembl ID:ENSOPRG00000010345
Aliases:None
Description:adenylate kinase 4 [Source:HGNC Symbol;Acc:363]


Retrocopy-Parental alignment summary:






>retro_opri_1094
ATGGCTTCTAAACTCCTGCCAGCAGTCATCCTCGGGCTGCCCGGCTCGGGAAAAGGCACCGTGTGCCAGATGATTGCCCA
GAATTTTGGCCTGCAGCACCTCTCCAGCGGCCACTTCTTGCGGGAGAACATCAAGGCCAACAGGGAAGTTGGTGATAATG
GCCAAGAAATACCTAGAGAGAGGCCCTTTTGGTCCCAGATCATGTCATCACACGCCTGATGCTCTCGGAGCTGGAGAGCA
GGAGTGGCCAGCACTGGCTTCTGGACGGCTTTCCGAGGACACTAGTACAGGCTGAAGCTTTAGACAAAATTTGTGACCTG
GATCTAGTGATCACTTTGAACATTCCGTTTGAGACGTTGAAAGATCGGCTCAACCGTCATTGGATTCACCCTCCCAGCGG
TAGAGTGTATAATATGGACTTCAACCCGCCTCATGTGCATGGAATTGATGACATCACTGGGGAAGCATTAATCCAACAAG
AGGAAGATAAGCCTGAAGCAGTTGCTGCGCGGCTAAGACGGTATAAGGACACTGCGAAGCCAGTCACTGAGCTATACAAG
AGCTGAGGAGTGCTCCACCAGTTTTCAGGGACGGAGACTAATAAAATATGGCCTTATGTTTACACACTTTCCTCAAACAA
GATCACACCTATTAAATGCAGACAGGCATTC

ORF - retro_opri_1094 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.56 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMASKLLRAV-LGPPGSGKGTVCQMIAQNFGLQHLSSGH-LRENIKTNTEVGG-MAKKYLERG-LLVPDHV
MASKLL.AV.LG.PGSGKGTVCQMIAQNFGLQHLSSGH.LRENIK.N.EVG..MAKKYLERG.LLVPDHV
RetrocopyMASKLLPAVILGLPGSGKGTVCQMIAQNFGLQHLSSGHFLRENIKANREVGD>MAKKYLERG>LLVPDHV
ParentalITRLMLSELESRSDQHWLLSGFPRTLAQAEALDKICDLDLVITLNIPFETLKDRLSRRWIHPPSGRVYNM
ITRLMLSELESRS.QHWLL.GFPRTL.QAEALDKICDLDLVITLNIPFETLKDRL.R.WIHPPSGRVYNM
RetrocopyITRLMLSELESRSGQHWLLDGFPRTLVQAEALDKICDLDLVITLNIPFETLKDRLNRHWIHPPSGRVYNM
ParentalDFNPPHVHGIDDITGEALIQQEEDKPEAVAARLRRYKDTAKPVIELYKSRGVLHQFSGTETNKIWPYVYT
DFNPPHVHGIDDITGEALIQQEEDKPEAVAARLRRYKDTAKPV.ELYKS.GVLHQFSGTETNKIWPYVYT
RetrocopyDFNPPHVHGIDDITGEALIQQEEDKPEAVAARLRRYKDTAKPVTELYKS*GVLHQFSGTETNKIWPYVYT
ParentalLFSNKITPVKRRQAF
L.SNKITP.K.RQAF
RetrocopyLSSNKITPIKCRQAF

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_1094 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 11 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000168351 retrocopy
Homo sapiens ENSG000001624336 retrocopies
Gorilla gorilla ENSGGOG000000266444 retrocopies
Myotis lucifugus ENSMLUG000000096221 retrocopy
Macaca mulatta ENSMMUG000000010793 retrocopies
Mus musculus ENSMUSG000000285271 retrocopy
Nomascus leucogenys ENSNLEG000000151633 retrocopies
Otolemur garnettii ENSOGAG000000160241 retrocopy
Ochotona princeps ENSOPRG00000010345 17 retrocopies
Pongo abelii ENSPPYG000000012696 retrocopies
Pan troglodytes ENSPTRG000000008274 retrocopies



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