RetrogeneDB ID:

retro_btau_1078

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:25:39692982..39694512(+)
Located in intron of:ENSBTAG00000030690
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSBTAG00000004054
Aliases:PAPOLA, PAPOLB
Description:Poly(A) polymerase alpha [Source:UniProtKB/Swiss-Prot;Acc:P25500]


Retrocopy-Parental alignment summary:






>retro_btau_1078
ATGCCGTTTCCGGTGACCACCCTGGGACCACAGCGGACCCCGCCGCCGCCCAAGCACTACGGCATCTCTTCCCCCATCAG
TTTAGCACCCCCCAGGGAGACTGACTGCATACTTACCCAGAAATTAATTGAAACTCTGAAGCCCTTCGGGGTTTTTGAAG
AGGAAGAGGAACTGCAGCGCAGGATTTTAATTTTGGAGAAATTAAATAATCTGGTAAAGGAATGGATACGAGAAATCAGT
GAAAGCAAGAGTCTTCCACAAGCTGTAATTGAAAATGTTGGAGGGAAAATCTTTACATTTGGTTCTTACAGGTTAGGGGT
GCATACGAAAGGTGCAGATATCGATGCGTTGTGCGTGGCACCGAGACACGTTGATCGAAGCGACTTTTTCACTTCCTTCT
ATGATAAATTGAAACTACATGAAGAAGTAAAGGATTTAAGGGCTGTTGAGGAGGCATTTGTACCAGTTATCAAACTCTGT
TTCGATGGGATAGAGATTGATATTTTGTTTGCAAGATTAGCACTGCAGACTATTCCTGAAGATTTGGACCTAAGAGATGA
CAGTCTGCTTAAAAACTTAGATATAAGATGCATAAGAAGCCTTAATGGTTGCCGGGTAACTGATGAGATTTTACATCTAG
TACCAAACATTGACAACTTCAGATTAACTCTGAGAGCCATCAAGCTGTGGGCCAAATGCCACAATATTTATTCCAATATA
CTAGGTTTCCTCGGTGGTGTTTCCTGGGCGATGCTAGTAGCAAGAACTTGCCAGCTTTATCCAAATGCCATAGCATCAAC
TCTTGTCCGTAAATTTTTCTTGGTGTTTTCTGAGTGGGAATGGCCGAATCCAGTGCTACTGAAAGAGCCCGAAGAACGGA
ATCTGAATTTGCCTGTCTGGGACCCAAGAGTAAGTCCCAGTGATAGGTACCATCTCATGCCCATAATCACACCAGCATAC
CCACAGCAGAACTCCACCTACAATGTGTCTGTTTCAACACGGATGGTCATGATTGAAGAGTTTAAGCAAGGGCTTGCTAT
CACACATGAGATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTTTTCGAAGCGCCCAGCTTCTTCCAGAAGTACAAGCATT
ATATTGTGCTTCTGGCAAGTGCGCCAACAGAGAAACAACATCTAGAGTGGGTGGGTTTGGTGGAATCAAAAATCCGAATT
CTGGTCGGAAGCTTGGAGAAGAATGAATTTATTACACTGGCTCATGTGAATCCTCAGTCGTTTCCAGCACCCAAGGAGAG
TCCTGACAAGGAAGAATTTCGTACAATGTGGGTGATTGGGTTAGTGTTAAAAAAACCAGAAAACTCTGAAGTTCTCAGTA
TTGACCTCACCTATGATATCCAGTCTTTCACAGACACTGTGTATAGGCAAGCGATAAATAGTAAAATGTTTGAGATGGAC
ATGAAAATTGCTGCAATGCATTTGAAAAGAAAGGAACTTCATCAACTACTGCCTAATCATGTGCTTCAGAAAAAGAAAAC
ACTTTCTACA

ORF - retro_btau_1078 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.14 %
Parental protein coverage: 69.01 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNN
MPFPVTT.G.Q.T.PP.KHYGI.SPISLA.P.ETDC.LTQKL.ETLKPFGVFEEEEELQRRILIL.KLNN
RetrocopyMPFPVTTLGPQRTPPPPKHYGISSPISLAPPRETDCILTQKLIETLKPFGVFEEEEELQRRILILEKLNN
ParentalLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
LVKEWIREISESK.LPQ.VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKL.
RetrocopyLVKEWIREISESKSLPQAVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLH
ParentalEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
RetrocopyEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
ParentalLHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
LHLVPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLV.KFFLVFS.WE
RetrocopyLHLVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWE
ParentalWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
WPNPVLLK.PEE.NLNLPVWDPRV.PSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.E
RetrocopyWPNPVLLKEPEERNLNLPVWDPRVSPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHE
ParentalILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
ILLSKAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
RetrocopyILLSKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
ParentalFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKR
FPAPKE.PDKEEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKIAAMH.KR
RetrocopyFPAPKESPDKEEFRTMWVIGLVLKKPENSEVLSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLKR
ParentalKQLHQLLPSHVLQKKKKHST
K.LHQLLP.HVLQKKK..ST
RetrocopyKELHQLLPNHVLQKKKTLST

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 1 .95 RPM 76 .93 RPM
ERP005899_muscle 1 .16 RPM 107 .11 RPM
SRP017611_brain 5 .16 RPM 79 .57 RPM
SRP017611_kidney 2 .79 RPM 126 .31 RPM
SRP017611_liver 1 .36 RPM 54 .22 RPM
SRP030211_testis 165 .57 RPM 200 .14 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_1078 retrocopy
EST ID Start End Identity Match Mis-match Score
CB432502 39693875 39694162 97.3 281 5 274
DY191781 39693075 39693308 98.8 229 3 226

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1078 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1078 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_30
Pan troglodytes retro_ptro_2595
Gorilla gorilla retro_ggor_202
Pongo abelii retro_pabe_3113
Macaca mulatta retro_mmul_1675
Callithrix jacchus retro_cjac_1763
Mus musculus retro_mmus_37
Rattus norvegicus retro_rnor_863
Canis familiaris retro_cfam_1783
Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000141421 retrocopy
retro_amel_517,
Bos taurus ENSBTAG00000004054 1 retrocopy
retro_btau_1078 ,
Canis familiaris ENSCAFG000000177831 retrocopy
retro_cfam_1783,
Callithrix jacchus ENSCJAG000000065122 retrocopies
retro_cjac_1763, retro_cjac_543,
Homo sapiens ENSG000000900601 retrocopy
retro_hsap_30,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Myotis lucifugus ENSMLUG000000109221 retrocopy
retro_mluc_1396,
Macaca mulatta ENSMMUG000000186101 retrocopy
retro_mmul_1675,
Monodelphis domestica ENSMODG000000128872 retrocopies
retro_mdom_1714, retro_mdom_1916,
Mustela putorius furoENSMPUG000000030541 retrocopy
retro_mputfur_1375,
Mus musculus ENSMUSG000000211111 retrocopy
retro_mmus_37,
Nomascus leucogenys ENSNLEG000000006251 retrocopy
retro_nleu_2771,
Otolemur garnettii ENSOGAG000000046111 retrocopy
retro_ogar_987,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,


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