RetrogeneDB ID:

retro_hsap_1813

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:20384644..20387327(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229586
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TNPO1
Ensembl ID:ENSG00000083312
Aliases:TNPO1, IPO2, KPNB2, MIP, MIP1, TRN
Description:transportin 1 [Source:HGNC Symbol;Acc:6401]


Retrocopy-Parental alignment summary:






>retro_hsap_1813
CAGCAAACCAAGGTGGAGTACGAATGGAAATCTGATAAGCAAGGGCTTCAGCAAATCCTGCAGCTATTGAAGGAGTCCCA
GTCCCCAGACACCACCATCCAGAGAACTGTGCAACAATTCTAGAAACTGGAACAACTTAATCAATATCCAGACTTTAGCA
ACTACTTGATTTTTGTTCTTACAAAATTAAAATCTGAAGATGAACCCACAAGTTCATTGCGTGGTCTCATCTTGAAGAAT
AATGTGAAAGCACACTTTCAGAACTTCCCAAATGGTGCAACAAACTTCATTAAAAGTGAATGTTTAAATAATATTGGTGA
CTCCTCTCTTCTGATTAGAGCCACTGTTGGTATTTCGATCACAGCTATAGCCTCCAAGAGAGAATTGCAGAATTGGCCTG
ACCTCTTACCAAAACTCTGTAGCCTGTTGGATTCTGACGATTACACCACCTGTGAGGGAGCATTTGGCACCCTTCAGAAG
ATTTGTGAAGATTCTGTTGAGATTTTAGATAGTGATGTTTTAGATTGTCCTCTCAACATCAGGATTCCCAAATTTTTACA
GTTCTTCAAGCACAGTAGTCCAAAAATAAGGTCTCACGCTGTTGTATGTGTCAATCAGTTTATCATCAGGACTCAAGCTC
TGATGTTGCACATTGATTCTTTTATTGAGAAATCTCTTTGCATTGGCTGGTGAGCCAGAGGTATGGAAAAATGTGTGCCG
AGCACTTGTGATGTTGTTCGAAGTTTGAGTGGATCGCCTGCTCCCTCACATGCGTAATATAGTTGAGTATATGCTACAGA
GGACTCAAGATCAAGATGAAAATGTGGCTTTAGAAGCCTGTGAATTTTGGCTAACTTTAGCTGAACAGCAAGTATGCAAA
GATGTATTCGTAAGGCATCTTCCCAGGTTGATTCCTGTGTTAGTGAATGGCATGAAGTACTCAGATATAGATATTATCCT
ACCTAAGGGTGATGTTGAAGAAGACGAAATGATTCCTGATAGTGAACAGGATATATGGCCACGTTTTCACCGATCAAGGA
CAGTGGCTCAGCAGCATGATGAAGATGGAATTGAAGAGGAAGATGATGATGATAATGAAATTGATGGTGATGATACAATT
TCTGACTGGAATCTAAGGAAATGTTCTGTTGCTGCCCTAGATGTTCTTGCAAACGTGCATCATGATGAACTGCTGCCATA
TATATTGCCCCTTTTGAAAGAATTACTTTTTCATCATGAATGGGTTGTTAAAGAATTAGCCATCTTGGGTTTAGGAACAG
TTGCTGAAGGTTTGCATGCAGGGCATGATTCCTTGCTTGCCTGAGCTTATTCCTCACCTTATTCAGTGCCTCTCTGATAA
AAAGGCTCTTGTCCGTTCCATAACATGCTGGACTCTTAGCCGCTATGCACACTGGGTAGTCAGCCAGCCACCAGACACGT
ACCTGAAGTCATTAATGACAGAGTTGCTAAAACGCATCCTGGATAGCAACAAGAGAGTACCAGAAGCTGCCTGCAGTGTC
TTTGCTACCCTAGAAGAGGAGGCTTGTACAGAACTTGTTGCTTACCTTGCTTATATACTTGATACCCTGGTCTTTGCATT
TAGTAAATACCAGCATAAGAACCTGCTCATTCTTTACAATGCCAGAGGGACATTAGCAGATTCAGTAGGACATCATTTAA
ACAAACCAGAATATATTCAAATGCTAATGCCTCCACTGATCCAGAAACGGAACATGTTAAAGGATGAAGATAAAGATCTT
TTCCCTTTACCTGAGTGTCCATTTTCAGTTGCCACGGTGCTGCAGTCTGGCTTCCTTCCATACTGTGAACCTATGTATCA
GCATTGGGTAAACCTAGTACAGAAGACTCTTGCACAAGCCATGCTAAGCAATGCTCAACCAGATCAATATGAAGCTCCAG
ATAAAGATTTTATGATAGTGGCTCTTGATTTACTGAGTGGCCTGGCTGAAGGACTTGGAGGCAATATTGAACAACTGGTA
GCCCGAAGTAACATCCTAACACTAACATATCAGTGCATGCAGGATAAAATGCCGGAAGTTCGACAGAGTTCTTTTGCCCT
GTTAAGTGACCTCACAAAAGCTTGCTTTCAGCATGTTAAGCCTTGTGTAGCTGATTTCATGCCAATATTGGGAACCAACC
TAACTCCAGAATTCATTTCAGTCTGCAACAATGACACATGAGCAATTGGAGAAATCTCCATTCAAATGGGTATAGAGATG
CAGCCTTATATTTACCCTATGGTGTTGCACCAGCTTGTAGAAATCATTAACAGACCCAACACACCAAAGACGTTGCTAAA
GAATACAGCAGTAACAATTGGTTGTCTTGGTTATGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTACGAGAC
CCTGGTGCACCTCTCTGAGAAACATAAGAGACAATGAGAAAAAGATTCAGCATTCCGTGGAATCTGCATCATGATCAGTG
TGAATCCCCATGGCATAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAACCCAAAAGATTATCTC
AGAGACATGTTCTGTAAGATCCTTCATGGATTTAAAAATCAAATTGGCAATGAAAATGGGAGGCATTTCTCTGACCAGTT
TCCTCTTCCCTTAAAAGAGCATCTTGCAGCTTTTTATGGTGTT

ORF - retro_hsap_1813 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.33 %
Parental protein coverage: 99.55 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalRQTKMEYEWKPDEQGLQQILQLLKESQSPDTTIQRTVQQ--KLEQLNQYPDFNNYLIFVLTKLKSEDEPT
.QTK.EYEWK.D.QGLQQILQLLKESQSPDTTIQRTVQQ..KLEQLNQYPDF.NYLIFVLTKLKSEDEPT
RetrocopyQQTKVEYEWKSDKQGLQQILQLLKESQSPDTTIQRTVQQF*KLEQLNQYPDFSNYLIFVLTKLKSEDEPT
ParentalRSLSGLILKNNVKAHFQNFPNGVTDFIKSECLNNIGDSSPLIRATVGILITTIASKGELQNWPDLLPKLC
.SL.GLILKNNVKAHFQNFPNG.T.FIKSECLNNIGDSS.LIRATVGI.IT.IASK.ELQNWPDLLPKLC
RetrocopySSLRGLILKNNVKAHFQNFPNGATNFIKSECLNNIGDSSLLIRATVGISITAIASKRELQNWPDLLPKLC
ParentalSLLDSEDYNTCEGAFGALQKICEDSAEILDSDVLDRPLNIMIPKFLQFFKHSSPKIRSHAVACVNQFIIS
SLLDS.DY.TCEGAFG.LQKICEDS.EILDSDVLD.PLNI.IPKFLQFFKHSSPKIRSHAV.CVNQFII.
RetrocopySLLDSDDYTTCEGAFGTLQKICEDSVEILDSDVLDCPLNIRIPKFLQFFKHSSPKIRSHAVVCVNQFII-
ParentalRTQALMLHIDSFIE-NLFALAGDEEPEVRKNVCRALVMLLEVRMDRLLPHMHNIVEYMLQRTQDQDENVA
RTQALMLHIDSFIE.NLFALAG..EPEV.KNVCRALVML.EV..DRLLPHM.NIVEYMLQRTQDQDENVA
RetrocopyRTQALMLHIDSFIE>NLFALAG--EPEVWKNVCRALVMLFEV*VDRLLPHMRNIVEYMLQRTQDQDENVA
ParentalLEACEFWLTLAEQPICKDVLVRHLPKLIPVLVNGMKYSDIDIILLKGDVEEDETIPDSEQDIRPRFHRSR
LEACEFWLTLAEQ..CKDV.VRHLP.LIPVLVNGMKYSDIDIIL.KGDVEEDE.IPDSEQDI.PRFHRSR
RetrocopyLEACEFWLTLAEQQVCKDVFVRHLPRLIPVLVNGMKYSDIDIILPKGDVEEDEMIPDSEQDIWPRFHRSR
ParentalTVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWVV
TVAQQHDEDGIEEEDDDD.EID.DDTISDWNLRKCS.AALDVLANV..DELLP.ILPLLKELLFHHEWVV
RetrocopyTVAQQHDEDGIEEEDDDDNEIDGDDTISDWNLRKCSVAALDVLANVHHDELLPYILPLLKELLFHHEWVV
ParentalKESGILVLGAIAEG-CMQGMIPYLPELIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLM
KE..IL.LG..AEG.CMQGMIP.LPELIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLK.LM
RetrocopyKELAILGLGTVAEG>CMQGMIPCLPELIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKSLM
ParentalTELLKRILDSNKRVQEAACSAFATLEEEACTELVPYLAYILDTLVFAFSKYQHKNLLILYDAIGTLADSV
TELLKRILDSNKRV.EAACS.FATLEEEACTELV.YLAYILDTLVFAFSKYQHKNLLILY.A.GTLADSV
RetrocopyTELLKRILDSNKRVPEAACSVFATLEEEACTELVAYLAYILDTLVFAFSKYQHKNLLILYNARGTLADSV
ParentalGHHLNKPEYIQMLMPPLIQKWNMLKDEDKDLFPLLECLSSVATALQSGFLPYCEPVYQRCVNLVQKTLAQ
GHHLNKPEYIQMLMPPLIQK.NMLKDEDKDLFPL.EC..SVAT.LQSGFLPYCEP.YQ..VNLVQKTLAQ
RetrocopyGHHLNKPEYIQMLMPPLIQKRNMLKDEDKDLFPLPECPFSVATVLQSGFLPYCEPMYQHWVNLVQKTLAQ
ParentalAMLNNAQPDQYEAPDKDFMIVALDLLSGLAEGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLG
AML.NAQPDQYEAPDKDFMIVALDLLSGLAEGLGGNIEQLVARSNILTL.YQCMQDKMPEVRQSSFALL.
RetrocopyAMLSNAQPDQYEAPDKDFMIVALDLLSGLAEGLGGNIEQLVARSNILTLTYQCMQDKMPEVRQSSFALLS
ParentalDLTKACFQHVKPCIADFMPILGTNLNPEFISVCNNATWAIGEISIQMGIEMQPYI-PMVLHQLVEIINRP
DLTKACFQHVKPC.ADFMPILGTNL.PEFISVCNN.T.AIGEISIQMGIEMQPYI.PMVLHQLVEIINRP
RetrocopyDLTKACFQHVKPCVADFMPILGTNLTPEFISVCNNDT*AIGEISIQMGIEMQPYIYPMVLHQLVEIINRP
ParentalNTPKTLLENTAITIGRLGYVCPQEVAPMLQQFIRPWCTSLRNIRDNE-EKDSAFRGICTMISVNPSGVIQ
NTPKTLL.NTA.TIG.LGYVCPQEVAPMLQQF.RPWCTSLRNIRDNE.EKDSAFRGIC.MISVNP.G.IQ
RetrocopyNTPKTLLKNTAVTIGCLGYVCPQEVAPMLQQFTRPWCTSLRNIRDNE<EKDSAFRGICIMISVNPHGIIQ
ParentalDFIFFCDAVASWINPKDDLRDMFCKILHGFKNQVGDENWRRFSDQFPLPLKERLAAFYGV
DFIFFCDAVASWINPKD.LRDMFCKILHGFKNQ.G.EN.R.FSDQFPLPLKE.LAAFYGV
RetrocopyDFIFFCDAVASWINPKDYLRDMFCKILHGFKNQIGNENGRHFSDQFPLPLKEHLAAFYGV

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 148 .51 RPM
bodymap2_adrenal 0 .00 RPM 114 .10 RPM
bodymap2_brain 0 .02 RPM 107 .10 RPM
bodymap2_breast 0 .00 RPM 164 .83 RPM
bodymap2_colon 0 .00 RPM 153 .87 RPM
bodymap2_heart 0 .07 RPM 113 .37 RPM
bodymap2_kidney 0 .00 RPM 162 .96 RPM
bodymap2_liver 0 .00 RPM 54 .77 RPM
bodymap2_lung 0 .00 RPM 141 .72 RPM
bodymap2_lymph_node 0 .00 RPM 144 .18 RPM
bodymap2_ovary 0 .00 RPM 158 .88 RPM
bodymap2_prostate 0 .00 RPM 181 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 92 .74 RPM
bodymap2_testis 0 .09 RPM 211 .25 RPM
bodymap2_thyroid 0 .00 RPM 192 .74 RPM
bodymap2_white_blood_cells 0 .00 RPM 179 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1813 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1813 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1813 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1813 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1813 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000083312 2 retrocopies
retro_hsap_1724, retro_hsap_1813 ,
Mus musculus ENSMUSG000000094701 retrocopy
retro_mmus_1501,
Pongo abelii ENSPPYG000000155451 retrocopy
retro_pabe_1528,
Pan troglodytes ENSPTRG000000169722 retrocopies
retro_ptro_1176, retro_ptro_3060,
Tursiops truncatus ENSTTRG000000002091 retrocopy
retro_ttru_1345,

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 = 0.02 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 .00 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 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 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 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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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