RetrogeneDB ID:

retro_opri_446

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_122852:815..1346(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KATNBL1
Ensembl ID:ENSOPRG00000010379
Aliases:None
Description:katanin p80 subunit B-like 1 [Source:HGNC Symbol;Acc:26199]


Retrocopy-Parental alignment summary:






>retro_opri_446
ACAGCTGGACAAGCTGTGAAAAGCCCAAACCTAGTAAGGTGATCTATCACAGAAAAATTCATCAGCCCTTTCCAGATCCT
CGTTACAGAAAAAAAAAAAAAAGAGTCCCTAGCAGTGTGGCTGTGACATGGCTAATAAAGGAAATGAACTGGCTTGTGCA
GGCCACTTGCCTGAAAAGTTATGTCATGATACTTGAACACACTTGATTAATTCCAGCGACACTGGTTCTTCACAGACTGT
AAGGCCATCATCAAAATACAGTGGGTTCTTAGCTGAGGTTACTCAGCACCATGAAACAATGGCCCAAGTTTTATCCAGCA
GGAATTTGAGATTAAATGTAGCCTTAACTTTTTGTAGGAAGAGAAGTGTAAGTGAGCTTGTAGCCTATTCGTGAGGACAG
AAGATCTTGGAGTTGTAGATTGTCCTCCTGTGTTCACCAGTAATATGCAGGAAGAAAAACACTACATCTCACCTGGCTGC
TGTGTGGACTTACTATTCTTAGTAAAGTCATCACTTAAAAGCAGATTTGAA

ORF - retro_opri_446 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.23 %
Parental protein coverage: 71.31 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTVGQAVKN-PDKLRKVIYRRKKVHHPFPDPCYRKKQSPSSG-GCDMANKENELACAGHLPEKLRHDSRTY
T.GQAVK..P........R......P.P.........PSS..GCDMANK.NELACAGHLPEKL.HD..T.
RetrocopyTAGQAVKS<PKPSKVIYHRKIHQPFPDPRYXXXXXXVPSSV<GCDMANKGNELACAGHLPEKLCHDT*TH
ParentalLINSSDSGSSQTESPSSKYSGFFSEVSQDHETMAQVLFSRNLRLNVALTFWRKRSISELVAY-LVRIEDL
LINSSD.GSSQT..PSSKYSGF..EV.Q.HETMAQVL.SRNLRLNVALTF.RKRS.SELVAY..VR.EDL
RetrocopyLINSSDTGSSQTVRPSSKYSGFLAEVTQHHETMAQVLSSRNLRLNVALTFCRKRSVSELVAY<FVRTEDL
ParentalGVVVDCLPVLTNSLQEEKHYISLGCCVDLLPLVKSLLKSRFE
G.VVDC.PV.T...QEEKHYIS.GCCVDLL.LVKS.LKSRFE
RetrocopyG-VVDCPPVFTSNMQEEKHYISPGCCVDLLFLVKSSLKSRFE

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_446 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 24 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000064132 retrocopies
Callithrix jacchus ENSCJAG000000211103 retrocopies
Cavia porcellus ENSCPOG000000111532 retrocopies
Dasypus novemcinctus ENSDNOG000000162795 retrocopies
Dipodomys ordii ENSDORG000000131722 retrocopies
Equus caballus ENSECAG000000234501 retrocopy
Echinops telfairi ENSETEG000000016407 retrocopies
Homo sapiens ENSG000001341523 retrocopies
Gorilla gorilla ENSGGOG000000142303 retrocopies
Macropus eugenii ENSMEUG000000156104 retrocopies
Myotis lucifugus ENSMLUG000000015322 retrocopies
Macaca mulatta ENSMMUG000000000131 retrocopy
Mustela putorius furoENSMPUG000000080191 retrocopy
Nomascus leucogenys ENSNLEG000000107722 retrocopies
Oryctolagus cuniculus ENSOCUG000000176545 retrocopies
Otolemur garnettii ENSOGAG000000156333 retrocopies
Ochotona princeps ENSOPRG00000010379 1 retrocopy
retro_opri_446 ,
Pongo abelii ENSPPYG000000063092 retrocopies
Pan troglodytes ENSPTRG000000068773 retrocopies
Sorex araneus ENSSARG000000078911 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000038131 retrocopy
Tupaia belangeri ENSTBEG000000016147 retrocopies
Tarsius syrichta ENSTSYG000000110591 retrocopy
Vicugna pacos ENSVPAG000000071701 retrocopy



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