RetrogeneDB ID:

retro_hsap_30

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:4899527..4901438(-)
Located in intron of:ENSG00000157927
Retrocopy
information
Ensembl ID:ENSG00000218823
Aliases:PAPOLB, PAPT, TPAP
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSG00000090060
Aliases:PAPOLA, PAP
Description:poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]


Retrocopy-Parental alignment summary:






>retro_hsap_30
ATGCCGTTTCCGGTGACAACCCAGGGACCACCGCAGCCGGCGCCGCCGCCGAATCGCTACGGCGTCTCCTCGCCTATCAG
TCTAGCGGTCCCCAAGGAGACGGACTGCCTCCTCACCCAGAGGCTAATAGAAACCCTCAGGCCCTTCGGGGTCTTCGAAG
AGGAAGAGGAACTGCAGCGCAGGATTTTAGTTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGCGAAATCAGT
GAAAGCAAGAGTCTTCCCCAGTCTGTAATTGAAAACGTTGGAGGAAAGATTTTTACGTTTGGCTCTTACAGATTAGGAGT
ACATACGAAAGGCGCAGATATTGACGCCTTGTGCGTTGCACCAAGTCATGTGGATCGAAGCGACTTTTTCACCTCATTCT
ATGCTAAACTGAAACTACAGGAGGAAGTGAAAGATTTAAGGGCTGTCGAGGAGGCATTTGTGCCAGTTATCAAACTGTGT
TTTGATGGGATAGAGATTGATATTTTATTTGCAAGATTAGCACTACAGACTATTCCAGAAGATTTGGACTTAAGAGATGA
CAGTCTACTTAAAAATTTAGACATTAGATGCATAAGAAGCCTTAATGGTTGCCGGGTAACCGATGAAATTTTACATCTAG
TGCCAAACATTGACAACTTCAGGCTGACTCTGAGAGCCATCAAACTGTGGGCCAAGTGCCACAATATCTATTCCAATATA
TTAGGTTTCCTCGGAGGTGTTTCCTGGGCCATGCTAGTAGCAAGAACTTGTCAGCTTTATCCAAATGCAGTAGCGTCAAC
TCTTGTACGGAAATTCTTCTTGGTATTTTCAGAATGGGAATGGCCAAACCCAGTGTTACTGAAGGAGCCTGAAGAACGGA
ATCTTAATTTGCCTGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCTATCATCACACCAGCATAC
CCACAGCAGAACTCCACATACAACGTGTCTATTTCAACCAGGATGGTCATGATTGAGGAGTTTAAACAGGGGCTTGCTAT
CACACACGAGATTTTGCTAAGTAAGGCAGAGTGGTCCAAACTCTTTGAAGCTCCAAGCTTCTTTCAAAAGTACAAGCATT
ATATTGTACTTCTGGCAAGTGCATCAACAGAAAAACAACATTTAGAATGGGTGGGCTTGGTGGAATCAAAGATCCGAATC
CTGGTTGGGAGCTTGGAGAAGAATGAATTTATTACACTGGCACATGTGAATCCACAGTCATTTCCAGCACCCAAAGAAAA
TCCTGATATGGAAGAATTTCGTACAATGTGGGTGATTGGGTTAGGGCTAAAAAAGCCAGATAATTCTGAAATTCTCAGCA
TTGATCTCACCTATGATATCCAGTCTTTCACAGATACTGTTTATAGGCAAGCAGTGAATAGTAAGATGTTTGAGATGGGT
ATGAAAATTACTGCAATGCATTTAAGAAGAAAGGAACTTCACCAGCTGCTGCCTCATCATGTGCTTCAGGACAAGAAAGC
ACACTCAACAGAAGGTAGAAGATTGACAGATTTGAACGACAGCAGCTTTGACTTGTCTGCAGGCTGTGAAAACAGCATGT
CTGTGCCTTCATCTACTAGCACTATGAAGACAGGCCCATTGATTAGCAGTTCTCAGGGTAGAAACAGTCCTGCCTTGGCT
GTAATGACAGCATCTGTGGCTAACATACAGGCTACTGAATTTTCCTTGCAACAGGTGAATACCAATGAAAGTTCAGGGGT
TGCATTAAACGAAAGTATTCCTCACGCTGTCTCTCAGCCTGCCATTTCTCCATCACCAAAGGCCATGGTCGCCAGAGTTG
TTTCTTCAACATGTCTCATAAGCCATCCAGACCTTCAGGAAACTCAGCAACAAACATATCTAATCCTATAG

ORF - retro_hsap_30 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.08 %
Parental protein coverage: 83.89 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNN
MPFPVTTQG..Q..PP...YG..SPISLA.PKETDC.LTQ.LIETL.PFGVFEEEEELQRRIL.L.KLNN
RetrocopyMPFPVTTQGPPQPAPPPNRYGVSSPISLAVPKETDCLLTQRLIETLRPFGVFEEEEELQRRILVLEKLNN
ParentalLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
LVKEWIREISESK.LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAP.HVDRSDFFTSFY.KLKLQ
RetrocopyLVKEWIREISESKSLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPSHVDRSDFFTSFYAKLKLQ
ParentalEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
RetrocopyEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
ParentalLHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
LHLVPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WE
RetrocopyLHLVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWE
ParentalWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
WPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS.STRMVM.EEFKQGLAIT.E
RetrocopyWPNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSISTRMVMIEEFKQGLAITHE
ParentalILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
ILLSKAEWSKLFEAP.FFQKYKHYIVLLASA.TEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
RetrocopyILLSKAEWSKLFEAPSFFQKYKHYIVLLASASTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
ParentalFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKR
FPAPKENPD.EEFRTMWVIGL..KK..NSE.LS.DLTYDIQSFTDTVYRQA.NSKMFE..MKI.AMH..R
RetrocopyFPAPKENPDMEEFRTMWVIGLGLKKPDNSEILSIDLTYDIQSFTDTVYRQAVNSKMFEMGMKITAMHLRR
ParentalKQLHQLLPNHVLQKKKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGRNSPA
K.LHQLLP.HVLQ.KK.HSTEG..LT.LNDSS.DLS....NSMSVPS.TS..KT.PL.S..SSQGRNSPA
RetrocopyKELHQLLPHHVLQDKKAHSTEGRRLTDLNDSSFDLSAGCENSMSVPSSTSTMKTGPLIS--SSQGRNSPA
ParentalPAVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPP
.AV..ASV.NIQATE.S..QVN..ESSG....ESIP....QPAISP.PK..V.RVVSST.L...P
RetrocopyLAVMTASVANIQATEFSLQQVNTNESSGVALNESIPHAVSQPAISPSPKAMVARVVSSTCLISHP

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
bodymap2_adipose 0 .00 RPM 158 .61 RPM
bodymap2_adrenal 0 .06 RPM 187 .15 RPM
bodymap2_brain 0 .12 RPM 100 .09 RPM
bodymap2_breast 0 .23 RPM 136 .85 RPM
bodymap2_colon 0 .00 RPM 264 .22 RPM
bodymap2_heart 0 .04 RPM 147 .41 RPM
bodymap2_kidney 0 .00 RPM 216 .61 RPM
bodymap2_liver 0 .00 RPM 99 .68 RPM
bodymap2_lung 0 .00 RPM 174 .75 RPM
bodymap2_lymph_node 0 .00 RPM 311 .33 RPM
bodymap2_ovary 0 .06 RPM 299 .56 RPM
bodymap2_prostate 0 .00 RPM 240 .77 RPM
bodymap2_skeletal_muscle 0 .00 RPM 93 .94 RPM
bodymap2_testis 24 .79 RPM 285 .45 RPM
bodymap2_thyroid 0 .00 RPM 188 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 355 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_30 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CQM POLR2A 7:4901284..4901764

EST - click to see more details

2 EST(s) were mapped to retro_hsap_30 retrocopy
EST ID Start End Identity Match Mis-match Score
CD299915 4899589 4900340 98.8 742 4 735
DB083939 4900193 4900745 100 552 0 552

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1761111816 libraries9 libraries4 libraries0 libraries0 libraries
TSS #2 TSS_1761121747 libraries75 libraries4 libraries1 library2 libraries

The graphical summary, for retro_hsap_30 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_30 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_30 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
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
Canis familiaris retro_cfam_1783
Parental genes homology:
Parental genes homology involve 20 parental genes, and 22 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 ENSG00000090060 1 retrocopy
retro_hsap_30 ,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Loxodonta africana ENSLAFG000000009461 retrocopy
retro_lafr_895,
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,
Procavia capensis ENSPCAG000000041991 retrocopy
retro_pcap_91,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Rattus norvegicus ENSRNOG000000048271 retrocopy
retro_rnor_863,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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