RetrogeneDB ID:

retro_cfam_1783

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:6:12792355..12794338(+)
Located in intron of:ENSCAFG00000016092
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSCAFG00000017783
Aliases:None
Description:poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]


Retrocopy-Parental alignment summary:






>retro_cfam_1783
CCGGTGACAACCCCGGGATCACAACAGATGCCGCTGCCTCCCAAGCACTATGGCATCTCTTCCCCCATCAGTTTAGCAGC
CCCCAAGGAGACTGACTGCGTACTTACCCAGAAGCTAATTGAAACCCTGAAGCCCTTTGGGGTTTTTGAAGAGGAAGAGG
AACTGCAGCGCAGGATTTTAATTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGAGAAATCAGTGAAAGCAAG
AGCCTTCCACAAGCTGTAATTGAAAACGTTGGAGGGAAAATCTTTACCTTTGGTTCTTACAGATTAGGAGTACATACAAA
AGGTGCCGATATTGATGCGTTGTGCGTTGCACCGAGACATGTCGATCGGAGCGACTTTTTCACCTCGTTCTATGACAAAT
TGAAACTACATGAAGAAGTAAAAGATTTAAGGGCTGTTGAGGAAGCATTTGTACCAGTTATTAAACTGTGTTTTGATGGG
ATAGAGATTGATATTTTGTTTGCAAGGTTGGCACTGCAGACTATTCCCGAAGATTTGGACCTGAGAGATGACAGTCTGCT
TAAAAACTTAGATATTAGATGCATAAGAAGCCTTAACGGTTGCCGGGTGACAGATGAAATTTTACATCTAGTACCAAACA
TTGACAACTTCAGGTTAACTCTGAGAGCCATCAAACTGTGGGCCAAATGCCACAATATCTATTCCAATATACTAGGCTTC
CTGGGAGGTGTTTCCTGGGCCATGCTAGTAGCAAGAACTTGCCAGCTCTACCCAAATGCTATAGCATCAACTCTTGTACG
GAAGTTTTTCTTGGTATTTTCTGAATGGGAGTGGCCAAATCCAGTGCTACTGAAAGAGCCTGAAGAGCGGAATCTTAATT
TGCCTGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCCATAATCACACCAGCATACCCACAGCAG
AACTCCACATACAATGTGTCTGTTTCGACAAGGATGGTCATGATTGAGGAGTTTAAACAAGGGCTTGCTATCACACATGA
AATTTTGCTCAGTAAGGCAGAGTGGTCCAAGCTTTTTGAAGCTCCGAGCTTCTTTCAAAAGTATAAGCATTATATTGTTC
TTCTAGCAAGCGCACCGACAGAAAAACAGCATCTTGAATGGGTGGGCTTGGTGGAATCAAAAATCCGAATCCTGGTTGGA
AGCTTGGAGAAGAATGAATTTATTACTCTGGCGCATGTGAATCCTCAGTCATTTCCAGCACCTAAGGAAAATCCTGACAA
GGAAGAATTTCGTACTATGTGGGTAATTGGGTTAGTGCTAAAAAAGCCAGAAAACTCTGACGTTCTCAGTATTGATCTCA
CCTATGATATCCAGTCTTTCACAGATACAGTTTATAGGCAAGCAATAAATAGCAAGATGTTTGAGATGGATATGAAAATT
GCTGCAATGCATTTAAAAAGAAAGGAACTTCATCAACTACTGCCTAATCATGTGCTTCAGAAACGGAAAACACATTCAAT
GGAAGGTGTCACTTTGACAGCTTTGAGTGATGGCAGCCTTGACTTGTCTGCAGCCAGTGAAGACAGCATGTCTGTGCCCT
CACCTACTGGCACTATGAAGACCAGCCCAGTGACTGGCAGCTCTCAGGGCAGAAATAGTCCTGTTCCTACTGTAATGGCT
GCATCTGTGACCACCGTACAAGTTACTGAAATTTCCTTGCAACAAGTGAATCCCAGTGAAAGCTTAGGGGGTGCATCGAG
TGAAAGCATTCCTCAGACTGCCTCACAACTAGCCCTTCCTCCACCACCAAAGCCCACAGTTGCCAGAGTTGTTTCTTCAG
CACGTCTGGTAAACCATCCACCCAGGCCTTCAGGGAGTCCTGCAACAAACATAGCTAATCCTATTGTGGGAGTCTAGGGG
ACGTTCTCACCTCATAAAGGACCAAGGAAACTTGAAAAGGAACAATCTCATAAAGAGACAAGT

ORF - retro_cfam_1783 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.33 %
Parental protein coverage: 88.99 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVK
PVTT.GSQQ...P.KHYGI.SPISLAAPKETDC.LTQKLIETLKPFGVFEEEEELQRRILIL.KLNNLVK
RetrocopyPVTTPGSQQMPLPPKHYGISSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILEKLNNLVK
ParentalEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEV
EWIREISESK.LPQ.VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKL.EEV
RetrocopyEWIREISESKSLPQAVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLHEEV
ParentalKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
RetrocopyKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
ParentalVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPN
VPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLV.KFFLVFS.WEWPN
RetrocopyVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWEWPN
ParentalPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILL
PVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.EILL
RetrocopyPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILL
ParentalSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
SKAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
RetrocopySKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
ParentalPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL
PKENPDKEEFRTMWVIGLV.KK.ENS..LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKIAAMH.KRK.L
RetrocopyPKENPDKEEFRTMWVIGLVLKKPENSDVLSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLKRKEL
ParentalHQLLPNHVLQKKKKHSTEGVRLTPLNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPAPAV
HQLLPNHVLQK.K.HS.EGV.LT.L.D.SLDLS..S..SMSVPSPT..MKTSP....GSSQGRNSP.P.V
RetrocopyHQLLPNHVLQKRKTHSMEGVTLTALSDGSLDLSAASEDSMSVPSPTGTMKTSPV--TGSSQGRNSPVPTV
ParentalTAASVTNPQATEVSVPQVNSTESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPPPRPSGNAA
.AASVT..Q.TE.S..QVN..ES.GG.SSESIPQTA.Q.A..PPPKPTV.RVVSS.RLVN.PPRPSG..A
RetrocopyMAASVTTVQVTEISLQQVNPSESLGGASSESIPQTASQLALPPPPKPTVARVVSSARLVNHPPRPSGSPA
ParentalTKIPNPIVGVKRTSSPHKEESPKKTKTEEDETS
T.I.NPIVGV..T.SPHK............ETS
RetrocopyTNIANPIVGV*GTFSPHKGPRKLEKEQSHKETS

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
SRP012049_cerebellum 0 .88 RPM 123 .85 RPM
SRP017611_brain 2 .54 RPM 74 .95 RPM
SRP017611_kidney 0 .73 RPM 87 .96 RPM
SRP017611_liver 0 .00 RPM 68 .74 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_cfam_1783 retrocopy
EST ID Start End Identity Match Mis-match Score
BM536718 12792319 12792807 99.6 486 2 484

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1783 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1783 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
Bos taurus retro_btau_1078
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 ENSBTAG000000040541 retrocopy
retro_btau_1078,
Canis familiaris ENSCAFG00000017783 1 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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