RetrogeneDB ID:

retro_pabe_3113

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:7:4899175..4900828(-)
Located in intron of:ENSPPYG00000017327
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSPPYG00000006128
Aliases:None
Description:poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]


Retrocopy-Parental alignment summary:






>retro_pabe_3113
AAGGAATGGATACGCGAAATCAGTGAAAGCAAGAGTCTTCCCCAGTCTGTAATTGAAAACGTTGGAGGAAAGATTTTTAC
GTTTGGCTCTTACAGATTAGGAGTACATACGAAAGGCGCAGATATTGACGCCTTGTGCGTTGCACCAAGTCATGTGGATC
GAAGCGACTTTTTCACCTCATTCTATGCTAAACTGAAACTACAGGAGGAAGTAAAAGATTTAAGGGCTGTTGAGGAGGCA
TTTGTGCCAGTTATCAAACTGTGTTTTGATGGGATAGAGATTGATATTTTATTTGCAAGATTAGCACTACAGACTATTCC
AGAAGATTTGGACCTAAGAGATGACAGTCTACTTAAAAATTTAGATATTAGATGCATAAGAAGCCTTAATGGTTGCCGGG
TAACCGATGAAATTTTACATCTAGTGCCAAACATTGACAACTTCAGGTTGACTCTGAGAGCCATCAAACTGTGGGCCAAG
TGCCACAATATCTATTCCAATATATTAGGTTTCCTCGGAGGTGTTTCCTGGGCCATGCTAGTAGCAAGAACTTGTCAGCT
TTATCCAAATGCAGTAGCGTCAACTCTTGTACGGAAATTCTTCTTGGTATTTTCAGAATGGGAATGGCCAAACCCAGTAT
TACTGAAGGAGCCTGAAGAACGGAATCTTAATTTGCCTGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTT
ATGCCTATCATCACACCAGCATACCCACAGCAGAACTCCACGTACAACGTGTCTATTTCAACCAGGATGGTCATGATTGA
GGAGTTTAAACAGGGGCTTGCTATCACACATGAGATTTTGCTAAGTAAGGCGGAGTGGTCCAAACTCTTTGAAGCTCCAA
GCTTCTTTCAAAAGTACAAGCATTATATTATACTTCTGGCAAGTGCATCAACAGAAAAACAACATTTAGAATGGGTGGGC
TTGGTGGAATCAAAGATCCGAATCCTGGTTGGGAGCTTGGAGAAGAATGAATTTATTACACTGGCACATGTGAATCCACA
GTCATTTCCAGCACCCAAAGAAAATCCTGATAAGGAAGAATTTCGTACAATGTGGGTGATTGGGTTAGGGCTAAAAAAGC
CAGAAAACTCTGAAATTCTCAGCATTGATCTCACCTATGATATCCAGTCTTTCACAGATACTGTTTATAGGCAAGCAATG
AATAGTAAGATGTTTGAGATGGGTATGAAAATTACTGCAATGCATTTAAGAAGAAAGGAACTTCACCAGCTGCTGCCTCA
TCATGTGCTTCAGGACAAGAAAGCACACTCAACAGAAGGTAGAAGATTGACAGATTTGAACGACAGCAGCTTTGGCTTGT
CTGCAGGCTGTGAAAACAGCATGTCTGTGCCTTCATCTACTAGCACTATGAAGACAGGCCCATTGATTAGCAGTTCTCAG
GGTAGAAACAGTCCTGCTCTGGCTATAATGACAGCATCTGTGGCTAACATACAGGCTACTGAAATTTCCTTGCAACAGGT
GAATACCAGTGAAAGTTCAGGGGTTGCATTAAACGAAAGTATTCCTCACGCTGTCTCTCAACCTGCCATTTCTCCATCAC
CAAAGGCCATGGTCGCCAGAGTTGTTTCTTCAACATGTCTCATAAGCCATCCA

ORF - retro_pabe_3113 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.53 %
Parental protein coverage: 76.07 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEELQRRILILGNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEE
.E..R.I.....LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAP.HVDRSDFFTSFY.KLKLQEE
RetrocopyKEWIREISESKSLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPSHVDRSDFFTSFYAKLKLQEE
ParentalVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILH
VKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILH
RetrocopyVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILH
ParentalLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWP
LVPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWP
RetrocopyLVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWEWP
ParentalNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEIL
NPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS.STRMVM.EEFKQGLAIT.EIL
RetrocopyNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSISTRMVMIEEFKQGLAITHEIL
ParentalLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP
LSKAEWSKLFEAP.FFQKYKHYI.LLASA.TEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP
RetrocopyLSKAEWSKLFEAPSFFQKYKHYIILLASASTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP
ParentalAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQ
APKENPDKEEFRTMWVIGL..KK.ENSE.LS.DLTYDIQSFTDTVYRQA.NSKMFE..MKI.AMH..RK.
RetrocopyAPKENPDKEEFRTMWVIGLGLKKPENSEILSIDLTYDIQSFTDTVYRQAMNSKMFEMGMKITAMHLRRKE
ParentalLHQLLPNHVLQKKKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGRNSPAPA
LHQLLP.HVLQ.KK.HSTEG..LT.LNDSS..LS....NSMSVPS.TS..KT.PL.S..SSQGRNSPA.A
RetrocopyLHQLLPHHVLQDKKAHSTEGRRLTDLNDSSFGLSAGCENSMSVPSSTSTMKTGPLIS--SSQGRNSPALA
ParentalVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPP
...ASV.NIQATE.S..QVN.SESSG....ESIP....QPAISP.PK..V.RVVSST.L...P
RetrocopyIMTASVANIQATEISLQQVNTSESSGVALNESIPHAVSQPAISPSPKAMVARVVSSTCLISHP

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 53 .52 RPM
SRP007412_cerebellum 0 .36 RPM 110 .54 RPM
SRP007412_heart 0 .00 RPM 63 .79 RPM
SRP007412_kidney 0 .00 RPM 67 .62 RPM
SRP007412_liver 0 .03 RPM 62 .21 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3113 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3113 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3113 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
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
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 ENSBTAG000000040541 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 ENSPPYG00000006128 1 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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