RetrogeneDB ID:

retro_ocun_156

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:19:33965105..33967127(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000010703
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSOCUG00000010466
Aliases:None
Description:kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]


Retrocopy-Parental alignment summary:






>retro_ocun_156
ATGGCCAGCCAGTTCTGTCTCCCTGTCGCCCCACACCCTTCATCCCTGAAACTCTTGAGGTCGCACTTCGAGGAGCTCCG
AGCGGGCCTCCGCATAGCAATCCAGCGCAGCGACAAGCGGATCCACCTCGCTGTGGTCACAGAGATTAACCAGGAGAACT
CGTGGGTCACGGTAGAGTGGGTGGAAAAAGGAGTCAAGAAAGGCAAAAAGATTGAGCTCGAGACCATATTCTTGCTGAAT
CCAGCTCTGGCTTCTGCGAAACACCCCAAGCAGGCCAGGCCCTTGCGCCCCGCGTCTCTCGTGCCATCTTCGGCCATCGG
GGACCAGCGTACAGCCACGCGGTGGATGGCAAGGATCTCCCCGAAAAGCGAAACCCCCTCAGGGGACAGCCCGGCGGTGG
GGGTGCCCAGCCACCCTTGCCTGGTGAAGCAGAAAAAGTCTCCCTGTGTACGGGAAATCGAGAAACTGCAGAAGCAGCGG
GAGCAGCGCCGGCGGCTGCAGCTGGAAATCCGATCCAGGCGTGCCCTGGACGTCAACGCGGGAAATCGCAACCATGAGAT
CATGTGCATGATCCAAGAGTGCCGCAGGCACCTGGACAGAAGCCTGATGTGCAGCCGGGAGCCCCCAGAAGACCACCGGA
TCTGTGTGTGCGTGAGGAAGCGGCCTCTCAACCAGCAAGAGACCACCATGAAGGACCTGGATATCATCACTATCCCCTCC
GACAAGGTGGTCATGGTGCACGAGTCCAAGCAAAAGGTGGACCTCACGCGCTACCTGGAGAACCAGATCTTCTGCTTCGA
CCATGCCTTTGACCACACCGCCTCCAACGAACTAGTGTACCAGTTCACCGCACAGCCGCTGGTGGAGTCCATCTTCCGGA
AGGGCATGGCCACCTGCTTTGCCTATGGGCAGACAGGCAGTGGGAAAACGCACACCATGGGGGGAGCCTTCTCGGGAAGA
GCCCAGGACTGCTCCAAAGGTATTTACGCCCTGGTGGCGCAGGATGTCTTTCTCTTGCTCAAAAACTCCACCTACGAGAA
GCTAGACCTCAAAGTCTACGGGACCTTCTTTGAGATTTATGGGGGCAAGGTGTATGATTTGCTGAACTGGAAGAAGAAAC
TGCAAGTCCTGGAGGACGGCCAGCAGCAAATCCAGGTGGTGGGTCTGCAGGAGCGGGAGGTGCGCTGTGTGGAGGAAGTG
CTGAACCTCGTGGGCCTGGGGAACAGCTGTCGGACGTCCGGGCAGACCTCGGTCAATGCCCAGTCCTCCAGGAGCCACGC
GGTGTTCCAGATCATCCTCAAGTCCGGAGGGAAACTGCACGGCAAGTTTTCCCTTGTCGACTTAGCTGGGAACGAACGGG
GAGCGGATACGGCCAAGGCCAACCGGAAGAGGCAGCTGGAAGGGGCGGAGATTAATAAGAGTCTGCTGGCTCTCAAAGAA
TGCATCCGGGCTCTGGGTCAGAACAAGCCGCACACCCCGTTCCGAGCCAGCAAGCTCACGCAGGTCCTTCGCGACTCCTT
TATAGGCCAGAACTCCTCCACTTGCATGATCGCCACTATCTCACCCGGGATGACCTCTTGTGAAAACACCCTCAACACGT
TGAGATACGCAAACAGAGTCAAAGAACTCACTATGGACGTAAGGTCCTACCATCGCTTTCTCTATCCTATGGGACATGAG
ACTCCGCAGATGCTGGAAAAACATCTCAGAAATTCCGAAGTGTCCCTTCAAAGAAATGAGTTTATGAAAACCCCTTGTAT
ACAGAGAGAGGAGGAGAAACAGAACAAAGAAGCTGACACCTTATCCACGCCGTTAACGAAGGATGCAGCCCCTTCTCAGA
AGGAATCTCCTGAATGGTGGCAGAACATCCAGGAGGCCGCTGATGGAGTAAACTATGACGTTGACTTTTGCATTGCCCAG
TCCTTGTCCATTTTGGAGCAGAAAATTGGTGTTCTGACTGAGATTCAAAAGAAACTGAAATTTTTACGTGATGACTTACA
GAAGAAGAGCAAAGTAGAGTGA

ORF - retro_ocun_156 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.94 %
Parental protein coverage: 55.65 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
..KS.CV.E.EKLQ..RE.RR..Q.E.R..RA.DV.A.N.N.EIMCMI...R..LD........P...HR
RetrocopyQKKSPCVREIEKLQKQREQRRRLQLEIRSRRALDVNAGNRNHEIMCMIQECRRHLDRSLMCSREPPEDHR
ParentalICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPLN..ET.MKDLD.ITIPS..VVMVHE.KQKVDLTRYLENQ.F.FD.AFD..A.NE.VY.FT
RetrocopyICVCVRKRPLNQQETTMKDLDIITIPSDKVVMVHESKQKVDLTRYLENQIFCFDHAFDHTASNELVYQFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKTHTMGG.FSG..QDCSKGIYAL.A.DVFL.LK...Y.KL.L.VY
RetrocopyAQPLVESIFRKGMATCFAYGQTGSGKTHTMGGAFSGRAQDCSKGIYALVAQDVFLLLKNSTYEKLDLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQEREV.CVE.VL.L...GNSCRTSGQTS.NA.SS
RetrocopyGTFFEIYGGKVYDLLNWKKKLQVLEDGQQQIQVVGLQEREVRCVEEVLNLVGLGNSCRTSGQTSVNAQSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQIIL...GKLHGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NKPHTP
RetrocopyRSHAVFQIILKSGGKLHGKFSLVDLAGNERGADTAKANRKRQLEGAEINKSLLALKECIRALGQNKPHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKE
FRASKLTQVLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVKE
RetrocopyFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKE

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 81 .18 RPM
SRP017611_kidney 0 .00 RPM 25 .95 RPM
SRP017611_liver 0 .00 RPM 11 .72 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_156 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_156 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_156 has 0 orthologous retrocopies within eutheria group .

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 ENSOCUG00000010466 1 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 ENSOPRG000000117681 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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