RetrogeneDB ID:

retro_btau_104

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:8:38922906..38926224(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000012168
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RANBP6
Ensembl ID:ENSBTAG00000039374
Aliases:None
Description:importin-5 [Source:RefSeq peptide;Acc:NP_001032906]


Retrocopy-Parental alignment summary:






>retro_btau_104
ATGGCGGCGTCCGGGTCTGCTGGAGTACCGGCGACCGTGTCGGGAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGTATGGTGCGGCGGCAGGCAGAGGAAATCTATGAAAATATCCCAGGTCTGTGTAAGACTACATTCCTCT
TAGATGCCGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCCCTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAAGTCTATCCAAATTTGCCTTCTGATGTTCAGAGGGACGTCAAGATTGAACTGATACTGGCTGTTAAGTT
AGAAACACATGCTAGTATGAGGAAAAAACTTTGTGACATTTTTGCAGTCCTGGCCAGGAATTTGATAGATGAGGATGGCA
CTAACCACTGGCCTGAAGGTCTGAAGTTCCTTGTTGATTCAATCTACTCTAAAAATGTGGTTCTATGGGAAGTTGCACTT
CACGTTTTCTGGCACTTTCCGGGGATTTTTGGGAACCAGGAGCGGCACGATTTGGATATCATCAAACGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCTGCTAGAGCTGCAGCTGCATTTGTACTTGCTAATGAGA
ATAATATTGGTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGATTCATGCTACCAGGAT
GATGATTCAGTGCTAGAATCCCTTGTCGAGATTGCAGATACTGTACCTAAATATTTGGGTCCTTATTTAGAAGATACTCT
GCAACTGAGTCTAAAGTTATGTGGAGACTCTAGACTTAGTAATCTGCAACGCCAGCTGGCACTTGAAGTAATAGTGACCT
TGTCTGAAACTGCCACCCCAATGTTGAAAAAACATACAAATATTATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGATCTACAAGATGACGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCATTAGACAGACTGGCTTGTGGGCTTGGTGGAAAACTTGTTTTACCAATGACTAAGGAGCATATCATGCAGA
TGCTGCAGAGCCCTGACTGGAAATACCGACATGCTGGATTAATGGCCTTATCTGCTATTGGAGAAGGATGCCATCAGCAA
ATGGAATCAATTTTAGATGAAACAGTTAACTCTGTTTTGCTTTTTCTTCAGGATCCTCATCCAAGGGTGAGGGCTGCAGC
CTGTACTACACTTGGACAGATGGCTACAGATTTTGCACCTAACTTCCAAAAGAAATTCCATGAAACTGTGATTGCAGCTC
TCTTGCGTACTATGGAAAATCAAGGTAATCAGCGTGTACAGTCACATGCAGCTTCTGCGCTTATTATTTTTATTGAAGAC
TGCCCCAAATCATTGCTGGTTCTATATTTGGATAGTATGTTAAGAAATCTACATTCCATCTTGGTGATTAAACTTCAAGA
GTTGATTCGCAATGGAACTAAGTTGGCCTTAGAACAGCTTGTGACAACCATTGCCTCAGTTGCAGATACAATAGAAGAAA
AATTTGTACCATACTATGATATATTTATGCCCTCACTAAAGCATACTGTTGAGCTTGCTGTTCAAAAGGAACTCAAACTT
CTGAAAGGAAAGACTATTGAATGCATTAGCCATGTTGGTCTTGCTGTTGGTAAGGAAAAATTTATGCAAGATGCATCAAA
TGTGATGCAGTTATTGTTGAAGACACAATCAGACTTAAATAATATGGAAGATGATGACCCTCAGACCTCTTACATGGTTT
CAGCATGGGCTAGAATGTGTAAAATTCTTGGAAGTGATTTTCAACAGTACCTTCCACTGGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGACGTTGCTCTCTTAGACACACAAGATGTGGAGAATATGAGTGATGATGATGGATGGCAATT
TGTAAATCTTGGAGACCAGCAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGTTGG
TTTATTATGCTAAGGAGTTAAGAGAAGGATTTATGGACTATACAGAACAAGTTGTAAAACTGATGGTTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCTGCAGAGTCCTTGCCTTTTCTCCTGGAATGTGCAAGAATTCGGGGGCC
AGAGTATCTTGCACAGATGTGGCAATTCATATGTGATCCCTTAATCAAGGCTATTGGGACCGAACCCGATACAGATGTAC
TCTCAGAAATAATGAATTCTTTTGCAAAATCCATTGAAGTAATGGGAGATGGGTGCCTTAATGATGAACACTTGGAAGAA
CTGGGAGAAATACTGAAAGCAAAACTTGAAGGGCACTTTAAAAACCAAGAACTAAGACAGGTTAAAAGACAGGAAGAAAA
CTATGATCAACAGGTTGAAATGTCTCTGCAAGATGAGGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTACAAGGAAAAGATTTTACCGTGGTTTGAACAGCTACTTCCATTAATTGTAAATCTAATT
TGTTCTAATAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATATTTGATGATATCATAGAGCACTGCAGTCCAACCTC
ATTTAAATATGTTGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGACAACAACCCTGAAGTCAGGCAAGCTGCTG
CTTATGGCCTGGGTGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCGCTGCTGGTG
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCTACAGAGAACTGTATCTCAGCAGTAGGGAAGAT
TTTGAGGTTTAAGCCTAACTGTGTAAACGTAGATGAAGTTCTTCCACACTGGTTGTCATGGCTTCCACTGCATGAGGATA
AAGAGGAAGCTATTCAGACTTTGAGTTTTCTCTGTGACTTAATTGAAAGTAACCACCCAGTTGTACTTGGTCCAAATAAT
TCCAATCTCCCAAAAATAATTAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAACTATGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTTGTACGTCAGGTACAGACTTCTGAAGAATTATGGTTGGAATGCATTTCCCATCTTGATGATGAGC
AGCAGGAAGCCTTACAGGAATTGCTAAATTTTGCTTGA

ORF - retro_btau_104 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.9 %
Parental protein coverage: 65.14 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSAMAAAAAEQQQFYLLLGNLLSPDNVVRKQAEETYENIPGQSKITFLLQAIRNTAAAEEARQMAAVLLRR
....A.....Q.FY.LL.NL..P...VR.QAEE.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRR
RetrocopyAGVPATVSGKQEFYQLLKNLINPSCMVRRQAEEIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRR
ParentalLLSSAFDEVYPTLPTDVQTAIKSELLMIIQMETQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFD
LLSS.F.EVYP.LP.DVQ...K.EL......ET..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.D
RetrocopyLLSSGFEEVYPNLPSDVQRDVKIELILAVKLETHASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLVD
ParentalSVSSQNMGLREAALHIFWNFPGIFGNQQQHYLDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNV
S..S.N..L.E.ALH.FW.FPGIFGNQ..H.LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.
RetrocopySIYSKNVVLWEVALHVFWHFPGIFGNQERHDLDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNI
ParentalALFKHFADLLPGFLQAVNDSCYQNDDSVLKSLVEIADTVPKYLRPHLEATLQLSLKLCGDTGLNNMQRQL
.LFK.FADLLPG.LQAVNDSCYQ.DDSVL.SLVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQL
RetrocopyGLFKDFADLLPGILQAVNDSCYQDDDSVLESLVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQL
ParentalALEVIVTLSETAAAMLRKHTNIVAQTIPQMLAMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMAC
ALEVIVTLSETA..ML.KHTNI.AQ..P..LAMMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.AC
RetrocopyALEVIVTLSETATPMLKKHTNIIAQAVPHILAMMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLAC
ParentalGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYA
GLGGKLVLPM.KEHIMQMLQ.PDWKYRHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.A
RetrocopyGLGGKLVLPMTKEHIMQMLQSPDWKYRHAGLMALSAIGEGCHQQMESILDETVNSVLLFLQDPHPRVRAA
ParentalACNAVGQMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDSLVKH
AC...GQMATDFAP.FQKKFHE.VIAALL.TME.QGNQRVQ.HAA.ALI.F.EDCPKSLL..YLDS....
RetrocopyACTTLGQMATDFAPNFQKKFHETVIAALLRTMENQGNQRVQSHAASALIIFIEDCPKSLLVLYLDSMLRN
ParentalLHSIMVLKLQELIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTI
LHSI.V.KLQELI..GTKL.LEQ.VT.IASVADT.EEKFVPYYD.FMPSLKH.VE.AVQKEL.LL.GKTI
RetrocopyLHSILVIKLQELIRNGTKLALEQLVTTIASVADTIEEKFVPYYDIFMPSLKHTVELAVQKELKLLKGKTI
ParentalECISLIGLAVGKEKFMQDASDVMQLLLKTQTDFSDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMG
ECIS..GLAVGKEKFMQDAS.VMQLLLKTQ.D...MEDDDPQ.SYM.SAWARMCKILG..FQQYLP.V..
RetrocopyECISHVGLAVGKEKFMQDASNVMQLLLKTQSDLNNMEDDDPQTSYMVSAWARMCKILGSDFQQYLPLVIE
ParentalPLMKTASIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVE
PL.KTAS.KP.VALLDTQD.ENMSDDDGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGF..
RetrocopyPLIKTASAKPDVALLDTQDVENMSDDDGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFMD
ParentalYTEQVVKLMVPLLKFYFHDDILI
YTEQVVKLMVPLLKFYFHD....
RetrocopyYTEQVVKLMVPLLKFYFHDNVRV

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 19 .32 RPM 52 .99 RPM
ERP005899_muscle 13 .62 RPM 274 .66 RPM
SRP017611_brain 33 .99 RPM 108 .31 RPM
SRP017611_kidney 27 .03 RPM 137 .15 RPM
SRP017611_liver 11 .10 RPM 60 .10 RPM
SRP030211_testis 7 .66 RPM 679 .71 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_btau_104 retrocopy
EST ID Start End Identity Match Mis-match Score
BG693420 38924892 38925360 99.6 466 2 464

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_104 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_104 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037841 retrocopy
retro_amel_3,
Bos taurus ENSBTAG00000039374 1 retrocopy
retro_btau_104 ,
Canis familiaris ENSCAFG000000055611 retrocopy
retro_cfam_452,
Choloepus hoffmanni ENSCHOG000000060611 retrocopy
retro_chof_11,
Cavia porcellus ENSCPOG000000048272 retrocopies
retro_cpor_265, retro_cpor_57,
Equus caballus ENSECAG000000148081 retrocopy
retro_ecab_37,
Felis catus ENSFCAG000000256571 retrocopy
retro_fcat_24,
Homo sapiens ENSG000000651501 retrocopy
retro_hsap_57,
Gorilla gorilla ENSGGOG000000087421 retrocopy
retro_ggor_47,
Loxodonta africana ENSLAFG000000161901 retrocopy
retro_lafr_22,
Myotis lucifugus ENSMLUG000000065001 retrocopy
retro_mluc_295,
Mus musculus ENSMUSG000000306622 retrocopies
retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys ENSNLEG000000078312 retrocopies
retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus ENSOCUG000000038981 retrocopy
retro_ocun_143,
Otolemur garnettii ENSOGAG000000075701 retrocopy
retro_ogar_169,
Pongo abelii ENSPPYG000000054581 retrocopy
retro_pabe_172,
Pan troglodytes ENSPTRG000000059842 retrocopies
retro_ptro_49, retro_ptro_745,
Pteropus vampyrus ENSPVAG000000045161 retrocopy
retro_pvam_8,
Rattus norvegicus ENSRNOG000000109891 retrocopy
retro_rnor_240,
Sus scrofa ENSSSCG000000095091 retrocopy
retro_sscr_24,
Ictidomys tridecemlineatus ENSSTOG000000111641 retrocopy
retro_itri_32,


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