RetrogeneDB ID:

retro_btau_180

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:19:3877038..3879090(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000017345
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSBTAG00000015022
Aliases:None
Description:kinesin-like protein KIF2A [Source:RefSeq peptide;Acc:NP_001070541]


Retrocopy-Parental alignment summary:






>retro_btau_180
ATGGCCAGCCAGTTATTCCGCCCTCTTACCCCGCGCCTCTCGTCCTTGACACCTGTGAAGCCGCATTTCGGACACCTCCA
AGCGGGCATCAGCGTGGCGATCCAGCGCACCGACGGGAGAATCCATCTCGCAGTGGTCACAGAGGTCAGACGGGACAACG
CTTGGGTCACGGTAGAGTGGGCCGAAAAAGGAGTCAAAAAAGGCAAAAAGGTTGCTTTAGAGACCATATTCCTGCTGAAT
CCAGCTCTGGCCTTGGCTGGGCCTGCCGCGCAGGGCAGGGCTTCGCGCTCCGTGTCTCTGGCGCCCCCTTCCGTTATCGG
GGACCAGCGAACAGCCGCGCGGTGGGCTGGGAAGATCCCCCAGAGAAACGAAACGCCCTCGGGGGACAGCCTGGCCGTGA
GAGTTCCCAGCAGCCCTTGCCTGATGACACAGCGGAAATCTGCCTGCCTACGAGAAATTGAGAAACTGCAGAAGCAGCGC
GAGAGGCGCCGACGGCTGCACCGCGAGATTCGCGCCCAGCGCGCCCGGGACGCAGATACTGGAAATGCCCACTATGAGAT
CCGGCGCCTGATCGAGGAGTGCCGCCGGCGCCTGCGCGGGGGCCGGATTTCCGGCCCTGAGCCGCGGGACGGCCGCCGCA
TCTGCGTCTGTGTGAGGAAGCGGCCTCTCAACAGGCAGGAGGCCACGCGGGAGGACCTAGATATCGTCACCATCCCCTCG
GACAACGTGGTCATGGTGCACGAGTCCAAGCAGAAGGTGGACCTCACTCGCTACCTGGAGAACCAGACCTTTTGCTTCGA
CCACGCTTTTGACGACACCGCCTCCAACGAGTTGGTGTATCAATTTACTGCCCAGCCGTTGGTTGAGTCCATCTTCCGCC
ATGGCATGGCCACCTGCTTTGCCTATGGACAGACAGGCAGCGGGAAAACGCACACTATGGGCGGAGGCTTTTCGGGAAGA
GACCAAGATTGTTCTAAAGGCATTTACGCCATGGTGGCGCAGGATGTTTTCCTCTTACTGAAAACTTCCGCTTATGAGAA
GCTGAACCTCAAAGTCTATGGGACGTTTTTTGAGATTTATGGGGGAAAGGTGTATGACTTGTTGAACTGGAAGAAGAAGC
TGCAAGTCCTTGAGGATGGCAGTCAACAAATCCAGGTAGTCGGGCTGCAGGAGCAGGAAGTGTGTTGTGTGGAAGACATG
CTGAACCTCGTGGAACTAGGGAACAGTTGCCGGACTTCAGGACAGACATCAGTCAATGCCCACTCTTCCAGGAGCCACGC
AGTGTTCCAGATCATTTTAAAGTCTCGAGGGAAACTGCATGGCAAGTTTTCCCTTGTTGACTTAGCTGGGAATGAAAGAG
GAGCAGATACTGCCAAGGCCAACCGGAAAAGACAGCTGGAAGGAGCAGAGATTAATAAGAGTCTCCTGGCACTCAAAGAA
TGCATCCGAGCTTTGGGTCAGAACAAGTCTCATACCCCATTCAGAGCCAGCAAGCTCACACAGGTGCTCCGGGACTCCTT
TATAGGCCAGAACTCCTCCACTTGCATGATTGCTACTATCTCTCCAGGGATGGCCTCTTGTGAAAATACCCTCAACACTT
TAAGATATGCAAATAGAGTAAAAGAAATAACTCTAAATTTAAGGCCTCGCCATCGTTGTCTTTATCCTGCTGAACGTGAA
ATGCCAAGGGTGTTGGAAAATCACATTAGAAATTCAGAAATGTCCCTTCAGGGGGATGAATTTATTAGAATACCTTGCCT
ACAGAGTGAGGAGGAGAAAGAGACTGAAGAAATCAAAGTGCTGTCCTCTCCATTAGTGGATACAACAATTTCCTGGAAGG
AAGCAAGCCAATGGCCAGATAATAAAATCCAGGATACATCTGATGAAGTAAACTGCAATGTTGACTTTTGCATTGCCCAG
TTATTGTCCATTTTGGAGAAGAAAATAGATATTCTGACTGAGATTCGAAGGAAACTGAAATTATTACAAGCTGACCTTCA
AAAGGAGAACAGGCATGGTGAAGTCAATGGTGAGAGATCAGACCTGAAATGA

ORF - retro_btau_180 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.2 %
Parental protein coverage: 61.06 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
.RKS.C..E.EKLQ..RE.RR....E.R..RA.D.D..N..YEI...I...R..L.........P.D..R
RetrocopyQRKSACLREIEKLQKQRERRRRLHREIRAQRARDADTGNAHYEIRRLIEECRRRLRGGRISGPEPRDGRR
ParentalICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPLN..E....DLD..TIPS..VVMVHE.KQKVDLTRYLENQTF.FD.AFDD.A.NE.VY.FT
RetrocopyICVCVRKRPLNRQEATREDLDIVTIPSDNVVMVHESKQKVDLTRYLENQTFCFDHAFDDTASNELVYQFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKTHTMGG.FSG..QDCSKGIYA..A.DVFL.LK...Y.KL.L.VY
RetrocopyAQPLVESIFRHGMATCFAYGQTGSGKTHTMGGGFSGRDQDCSKGIYAMVAQDVFLLLKTSAYEKLNLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQE.EV.CVED.L.L...GNSCRTSGQTS.NAHSS
RetrocopyGTFFEIYGGKVYDLLNWKKKLQVLEDGSQQIQVVGLQEQEVCCVEDMLNLVELGNSCRTSGQTSVNAHSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQIIL...GKLHGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NK.HTP
RetrocopyRSHAVFQIILKSRGKLHGKFSLVDLAGNERGADTAKANRKRQLEGAEINKSLLALKECIRALGQNKSHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKELTVD
FRASKLTQVLRDSFIG.NS.TCMIATISPGMASCENTLNTLRYANRVKE.T..
RetrocopyFRASKLTQVLRDSFIGQNSSTCMIATISPGMASCENTLNTLRYANRVKEITLN

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
ERP005899_liver 0 .00 RPM 5 .34 RPM
ERP005899_muscle 0 .00 RPM 17 .31 RPM
SRP017611_brain 0 .00 RPM 70 .39 RPM
SRP017611_kidney 0 .00 RPM 25 .72 RPM
SRP017611_liver 0 .00 RPM 6 .57 RPM
SRP030211_testis 80 .27 RPM 128 .11 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

2 EST(s) were mapped to retro_btau_180 retrocopy
EST ID Start End Identity Match Mis-match Score
DT829799 3876965 3877507 99.3 538 4 534
EH125619 3876929 3877705 99.9 775 1 774

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_180 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_180 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_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 ENSBTAG00000015022 1 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 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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