RetrogeneDB ID:

retro_opri_486

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_13680:189..738(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPNS1
Ensembl ID:ENSOPRG00000016562
Aliases:None
Description:calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]


Retrocopy-Parental alignment summary:






>retro_opri_486
CGGATAGTCGGAGGGATTGTGAATTTTATCAGTGAAGCTGCAGCAGCTCAGTATACTCCAGAACCACCTCCCCCTCAGAA
GCACTTCACCCATGTGGAGGCCCATGAAAGCGAAGAAGAGAGGCGATTTCGGCGACAGTTTGAGCAACTGGCCGGTCCAG
ACCTGGAGGTGGGTGCCACCGACCTGATGAATATTCTCAACAAAGTCATCTCTAAACACAAGGAGACCCTGAAGACAGAC
AGCTTCAGCCTTGACACGTGCCGGAGCATTGTGTCTGTCATGGACAGTGACACGAACGGGAAGCTGGGCTTTGAAGAATT
CAAGTACCTGTGGAACAACATTAAGAAGTGGCAGTGTGTGTATAAGCAGTACGACAAGGATAGCTCTGGGTGTCTGCGTG
GTTCCCAGCTGCGGCAGGCTGTGCAGGCAGCAGGCTTCCAGCTGAACGAGCAGATCCACGAAATGATCGTGCGCCGCTAC
ACTGATGAGGATGGCAGTATGGATTTTAACAACTTCATCAGCTGCCTTGTCCGCCTGGACGGCATGTTT

ORF - retro_opri_486 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.57 %
Parental protein coverage: 78.02 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRILGGVISAISEAAA-QNNLEPPPPRSHYSNIEANESEEVRQFRKLFAQLAGDDMEVSATELMNILNKVV
RI.GG....ISEAAA.Q...EPPPP..H....EA.ESEE.R.FR..F.QLAG.D.EV.AT.LMNILNKV.
RetrocopyRIVGGIVNFISEAAAAQYTPEPPPPQKHFTHVEAHESEEERRFRRQFEQLAGPDLEVGATDLMNILNKVI
ParentalTRHPD-LKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDMDRSGTICSSELPGA
..H...LKTD.F..DTCRS.V.VMDSDT.GKLGFEEFKYLWNNIKKWQ..YKQ.D.D.SG....S.L..A
RetrocopySKHKETLKTDSFSLDTCRSIVSVMDSDTNGKLGFEEFKYLWNNIKKWQCVYKQYDKDSSGCLRGSQLRQA
ParentalFEAAGFHLNTHLYNMIIRRYSDESGNMDFDNFISCLVRLDAMF
..AAGF.LN.....MI.RRY.DE.G.MDF.NFISCLVRLD.MF
RetrocopyVQAAGFQLNEQIHEMIVRRYTDEDGSMDFNNFISCLVRLDGMF

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_486 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 22 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000005111 retrocopy
Ailuropoda melanoleuca ENSAMEG000000010241 retrocopy
Bos taurus ENSBTAG000000148722 retrocopies
Canis familiaris ENSCAFG000000313141 retrocopy
Equus caballus ENSECAG000000122101 retrocopy
Echinops telfairi ENSETEG000000076502 retrocopies
Felis catus ENSFCAG000000141491 retrocopy
Microcebus murinus ENSMICG000000102551 retrocopy
Myotis lucifugus ENSMLUG000000249441 retrocopy
Macaca mulatta ENSMMUG000000002492 retrocopies
Monodelphis domestica ENSMODG000000141791 retrocopy
Mustela putorius furoENSMPUG000000056171 retrocopy
Oryctolagus cuniculus ENSOCUG000000130931 retrocopy
Otolemur garnettii ENSOGAG000000069921 retrocopy
Ochotona princeps ENSOPRG00000016562 2 retrocopies
retro_opri_181, retro_opri_486 ,
Procavia capensis ENSPCAG000000063531 retrocopy
Pelodiscus sinensis ENSPSIG000000127931 retrocopy
Pteropus vampyrus ENSPVAG000000128853 retrocopies
Rattus norvegicus ENSRNOG000000457472 retrocopies
Sorex araneus ENSSARG000000042661 retrocopy
Sus scrofa ENSSSCG000000301492 retrocopies
Vicugna pacos ENSVPAG000000080741 retrocopy



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