RetrogeneDB ID:

retro_opri_815

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_3379:169243..170590(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOPRG00000012985
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSOPRG00000011768
Aliases:None
Description:kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]


Retrocopy-Parental alignment summary:






>retro_opri_815
CAGAAAAAGTCTCCCTGCTTACGGGAAATTGAGAAACTGCAGAAGCAGCGGGAGCAGCGTCAGCAGCTCCATCTGGAAAT
CCGATCTAGGCGTGCCCTGGACATCAACAGGGGAAACCGCAACCATGAGATCATGTGCATGATCGAGGAGTACCGCAGGC
ACCTGGATAAAAACGTGCTGTGCAGCTGTGAGCCCCCAGAAGACCACCGAATCTGCGTCTGCGTGAGGAAGCGGCCCCTC
AACCAGCGTGAGACCACCATGAAAGACTTGGATATCATCACCATCCCCTCGGACAAAGTGGTCATGGTGCACGAGTCCAA
GCAAAAGGTGGACCTCACGCGCTACCTGGAGAACCAGATATTCTGCTTTGACCATGCCTTTGATGACACTGCCTCCAATG
AACTAGTGTACCAGTTCACAGCGCAGCCGCTGGTGGAGTCCATCTTTCGCAAGGGCATGGCCACCTGCTTTGCCTATGGG
CAGACAGGTAGTGGGAAAACACACACCATGGGAGGAGCTTTCTCTGGAAAGGCACAGAACTGTTCCAAAGGTATTTATGC
CTTGGTCGCACAGGATGTCTTTCTCTTGCTCAAAAACCCGACTTATGAGAAGTTCGACCTTAAAGTCTACGGGACGTTCT
TTGAGATTTACGGGGGCAAGGTGTATGACCTGCTGAACTGGAAGAAGAAGCTGCAGGTCCTGGAGGACGGCCATCAGCAA
ATCCAAGTGGTGGGGCTGCAGGAGCGGGAGGTGTGCTGCGTGGAGGAAGTGTTGAGCCTGGTGGAGCTGGGGAACAGCTG
TCGGACTTCAGGGCAGACCTCAGTCAATGCCCAGTCCTCCAGGAGCCACGCAGTGTTCCAGATCATCCTGAAGTCAAGAG
GGAAACTGCATGGAAAGTTTTCCCTGGTTGACTTGGCTGGGAATGAAAGGGGAGCAGACACAGCCAGGGCCAATCGGAAG
AGACAGCTGGAAGGGGCAGAGATTAATAAGAGCCTCCTAGCTCTCAAAGAGTGCATCAGGGCTTTGGGGAAGAACAAGCC
TCACACCCCATTCAGAGCCAGCAAACTCACACAGGTGCTCAGGGACTCCTTCATAGGGCAGAACTCCTCCACCTGCATGA
TCGCCACCATCTCCCCAGGGATGACCTCCTGTGAGAACACCCTCAACACCCTGAGATACGCACATAGGGTGAAAGCGCTC
ACCTTGGATATGAGGTGTTGTCCTCGTAGCCTCTGTCCCGTGGGACACGAGGCTCCACAGTTGTTGGAAAAACAGTCCAA
GAATTCAGATATGTCCCTCCAGAGGCACGAATTTATGAAAACGCCTTGCATGCAGAACGACGAGGAT

ORF - retro_opri_815 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.7 %
Parental protein coverage: 67.32 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPXXXXX
..KS.C..E.EKLQ..RE.R.....E.R..RA.D....N.N.EIMCMI...R..LD...L....P.....
RetrocopyQKKSPCLREIEKLQKQREQRQQLHLEIRSRRALDINRGNRNHEIMCMIEEYRRHLDKNVLCSCEPPEDHR
ParentalXXXXXXXXXXXXXXTQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
..............T.MKDLD.ITIPS..VVMVHE.KQKVDLTRYLENQ.F.FD.AFDD.A.NE.VY.FT
RetrocopyICVCVRKRPLNQRETTMKDLDIITIPSDKVVMVHESKQKVDLTRYLENQIFCFDHAFDDTASNELVYQFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKTHTMGG.FSGK.Q.CSKGIYAL.A.DVFL.LK.P.Y.K..L.VY
RetrocopyAQPLVESIFRKGMATCFAYGQTGSGKTHTMGGAFSGKAQNCSKGIYALVAQDVFLLLKNPTYEKFDLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQEREV.CVE.VL.L...GNSCRTSGQTS.NA.SS
RetrocopyGTFFEIYGGKVYDLLNWKKKLQVLEDGHQQIQVVGLQEREVCCVEEVLSLVELGNSCRTSGQTSVNAQSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQIIL...GKLHGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NKPHTP
RetrocopyRSHAVFQIILKSRGKLHGKFSLVDLAGNERGADTARANRKRQLEGAEINKSLLALKECIRALGKNKPHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKELTVDPTAAGDVRPVIHHPPSQ
FRASKLTQVLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYA.RVK.LT.D............H...Q
RetrocopyFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYAHRVKALTLDMRCCPRSLCPVGHEAPQ
ParentalIDDVEAQWGVGSSPQRDDLKLLCEQNEEE
...........S.......K..C.QN.E.
RetrocopyLLEKQSKNSDMSLQRHEFMKTPCMQNDED

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

retro_opri_815 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 30 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000095191 retrocopy
retro_apla_3,
Bos taurus ENSBTAG000000150221 retrocopy
retro_btau_180,
Choloepus hoffmanni ENSCHOG000000078881 retrocopy
retro_chof_1348,
Cavia porcellus ENSCPOG000000093931 retrocopy
retro_cpor_72,
Dipodomys ordii ENSDORG000000063351 retrocopy
retro_dord_763,
Equus caballus ENSECAG000000198101 retrocopy
retro_ecab_32,
Homo sapiens ENSG000000687961 retrocopy
retro_hsap_69,
Gorilla gorilla ENSGGOG000000047741 retrocopy
retro_ggor_68,
Macaca mulatta ENSMMUG000000003991 retrocopy
retro_mmul_145,
Monodelphis domestica ENSMODG000000196051 retrocopy
retro_mdom_242,
Mus musculus ENSMUSG000000216931 retrocopy
retro_mmus_68,
Nomascus leucogenys ENSNLEG000000028651 retrocopy
retro_nleu_2329,
Oryctolagus cuniculus ENSOCUG000000104661 retrocopy
retro_ocun_156,
Otolemur garnettii ENSOGAG000000005275 retrocopies
retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps ENSOPRG00000011768 1 retrocopy
retro_opri_815 ,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG000000140002 retrocopies
retro_rnor_1284, retro_rnor_47,
Sorex araneus ENSSARG000000077681 retrocopy
retro_sara_457,
Sarcophilus harrisii ENSSHAG000000019501 retrocopy
retro_shar_30,
Ictidomys tridecemlineatus ENSSTOG000000127101 retrocopy
retro_itri_40,
Tupaia belangeri ENSTBEG000000093961 retrocopy
retro_tbel_761,
Tarsius syrichta ENSTSYG000000021151 retrocopy
retro_tsyr_1791,
Vicugna pacos ENSVPAG000000088641 retrocopy
retro_vpac_572,
Drosophila melanogaster FBgn00302682 retrocopies
retro_dmel_1, retro_dmel_2,


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