RetrogeneDB ID:

retro_rnor_47

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:10:78940904..78942899(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000002535
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Kif2a
Ensembl ID:ENSRNOG00000014000
Aliases:Kif2a, Kif2
Description:kinesin-like protein KIF2A [Source:RefSeq peptide;Acc:NP_445828]


Retrocopy-Parental alignment summary:






>retro_rnor_47
ATGGCCAGCCAGTTCTGCCTTCCTCTGGCCCCACGCCTCTCACCCCTTAAACCTCTGAAATCCCACTTCACAGACTTCCA
GGTGGGCATCTGTGTGGCGATCCAGCGCAGTGACAAACGGATTCATCTGGCTGTGGTCACAGAGATCAACCGAGAAAACT
CCTGGGTCACGGTAGAGTGGGTTGAGAAAGGAGTCAAAAAAGGAAAGAAGATTGAACTGGAGACTGTACTTCTGTTGAAC
CCTGCTTTGGCTTCTACTGAACACCAACGGTCACGTAGACCCCTGCGCCCAGTGTCTGTAATACCCGCTACTGCCATTGG
AGACCAGCGAACAGCCACCAAATGGATTGCGATGATTCCACACAGAAATGAAACACCCTCAGGGGACAGCCAAACCCTGG
TGATCCCCAGCAACCCTTGTCTGATGAAGCGGAAAAAATCCCCCTGCCTACGGGAAATTGAAAAGCTGCAGAAGCAGAGA
GAGAAGCGCCGACGACTGCAGCTAGAGATCCGAGCTAGACGAGCCCTTGACATCAACACTGGAAATCCAAACTTTGAGAC
TATGCGCATGATTGAGGAGTACCGCAGGCATCTAGACAGCAGCAAGATGTCCCGCCTGGAGCCCCCAGAAGACCACCGCA
TCTGTGTGTGTGTGAGGAAGCGCCCTCTTAATGAGAGGGAGACCACCATGAAGGACTTAGATATCATCACTATTCCCTCG
CACAATGTGGTCATGGTACACGAGTCTAAACAAAAGGTGGACCTGACCCGCTACTTGGAAAACCAGACCTTCTGTTTTGA
CCATGCCTTTGATGACACGGCATCTAATGAATTAGTTTACCAGTTCACCGCCCGGCCTCTTGTGGAGTCCATCTTCCGGA
AGGGCATGGCCACTTGCTTTGCCTATGGGCAGACTGGCAGTGGAAAAACCCACACAATGGGTGGAGCCTTTTCAGGAAAG
GCCCAAGAGTGTTCTAAAGGGATTTATGCCCTGGTAGCTCAGGATGTCTTCCTCCTCCTAAGAACCCCTGCCTATGAGAA
ATTGGAGCTCAAAGTCTACGGGACCTTTTTTGAGATCTATGGTGGCAAAGTGTACGATCTGCTAAACTGGAAGAAGAAGC
TGCAAGTCCTGGAGGATGGAAATCAGCAAATACAAGTGGTAGGACTGCAGGAGCAGGAGGTGGGCTGTGTGGAGGAAGTC
CTGAATCTGGTGGAGCTCGGAAACAGCTGTCGGACTTCCGGTCAGACCTCTGTCAACGCCCACTCATCCAGGAGCCACGC
TGTGTTCCAGCTCATTCTCAAGTGCGGAGGGAAACTGCACGGCAAGTTTTCCCTCGTTGACTTAGCTGGGAACGAAAGGG
GAGCAGATACTGCCAAGGCTACCCGGAAGAGGCAGCTGGAAGGGGCTGAGATAAATAAAAGTCTGCTAGCTCTAAAAGAG
TGCATCAGGGCTTTGGGTAAGAACAAGTCTCATACCCCATTCAGAGCGAGCAAACTCACACAGGTACTCCGGGACTCCTT
CATAGGGCAGAACTCCTATACTTGCATGATCGCTACAATCTCGCCCGGGATGACTTCCTGTGAAAACACCCTCAATACTT
TAAGATATGCAAACAGAGTCAAAGAATTGGCTTTAGAAGCAAGGCCTTACCCTCCAACTGACCATGAAATGCCACTAACG
TTAGAAAACGGCAATACAAATTCGGAAAAGTCCCTTCAGAAGGATGACATCATTCAAATACCAACTGTACAGAAAGAGGA
AGAGAAAGAAAGCGATGAACTCACATCAACAAAGGAGCCAGCAGCTTCATGGAGCAGGTCCGGTCCATGGTGGGAGGCCA
TCCAGGAAACGGCTGAGGGAGTTAACTGTGATGTGGATTTTTGCATTGCGCAGTCTTTGTCCATTTTGGAGCAGAAAATT
GGTGTGCTGACTGAGATCCAAAAGAAGCTCCAATTGCTACGAGATGACCTCCAAAAGAAAAGCCAAGCTGAGTGA

ORF - retro_rnor_47 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.44 %
Parental protein coverage: 63.64 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
R.KS.C..E.EKLQ..REKRR..Q.E.R..RA.D....NPN.E.M.MI...R..LD........P...HR
RetrocopyRKKSPCLREIEKLQKQREKRRRLQLEIRARRALDINTGNPNFETMRMIEEYRRHLDSSKMSRLEPPEDHR
ParentalICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPLN..ET.MKDLD.ITIPS..VVMVHE.KQKVDLTRYLENQTF.FD.AFDD.A.NE.VY.FT
RetrocopyICVCVRKRPLNERETTMKDLDIITIPSHNVVMVHESKQKVDLTRYLENQTFCFDHAFDDTASNELVYQFT
ParentalARPLVETIER-GMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
ARPLVE.I.R.GMATCFAYGQTGSGKTHTMGG.FSGK.Q.CSKGIYAL.A.DVFL.L..P.Y.KLEL.VY
RetrocopyARPLVESIFRKGMATCFAYGQTGSGKTHTMGGAFSGKAQECSKGIYALVAQDVFLLLRTPAYEKLELKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQE.EV.CVE.VL.L...GNSCRTSGQTS.NAHSS
RetrocopyGTFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEQEVGCVEEVLNLVELGNSCRTSGQTSVNAHSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQ.IL...GKLHGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NK.HTP
RetrocopyRSHAVFQLILKCGGKLHGKFSLVDLAGNERGADTAKATRKRQLEGAEINKSLLALKECIRALGKNKSHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKELTVDPTAAGDVRPIMHHPPSQ
FRASKLTQVLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVKEL......A....P..H..P..
RetrocopyFRASKLTQVLRDSFIGQNSYTCMIATISPGMTSCENTLNTLRYANRVKELALE---ARPYPPTDHEMPLT
ParentalIDDLETQWGVGSSPQRDD-LKLLCEQNEEE
.....T......S.Q.DD.......Q.EEE
RetrocopyLENGNT--NSEKSLQKDDIIQIPTVQKEEE

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 59 .96 RPM
SRP017611_kidney 0 .00 RPM 17 .72 RPM
SRP017611_liver 0 .00 RPM 5 .58 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_47 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_47 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_47 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_68
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 ENSOPRG000000117681 retrocopy
retro_opri_815,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG00000014000 2 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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