RetrogeneDB ID:

retro_hsap_4080

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:79672379..79674649(-)
Located in intron of:ENSG00000104432
Retrocopy
information
Ensembl ID:ENSG00000253919
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRKRIR
Ensembl ID:ENSG00000137492
Aliases:PRKRIR, DAP4, P52rIPK, THAP0, THAP12
Description:protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) [Source:HGNC Symbol;Acc:9440]


Retrocopy-Parental alignment summary:






>retro_hsap_4080
TGCCGCCAACTGCACGCGGAAGAGCACGCAGTCCGACTTGACTTGGCCTTCTTCAGCTTCCCGCGGGACCCTGCCAGATG
CCAGAAGTGGGTGGAGAACTGTAGGAGAGCAGACTTAGAAGATAAAACACCTGATCAGCTAAATAAACATTATCGATTAT
GTGCCAAACATTTTGAGACCTCTATGATCTGTAGAACTGGTCCTTATAGGACAGTTCTTCGAGATAATGCAATACCAACA
ATATTTGATCTTAACAGTCATTTGAACAACCCACATAGTAGACACAGAAAACGAATAAAAGAACTGAGTGAAGATGAAAT
CAGGACACTGAAACAGAAAAAAATTGATGAAACTTCTGAGCAGGAACAAAAACATAAAGAAACCAACAATAGCAATGCTC
AGAACCCCAGCGAAGAAGAGGGTGAAGGGCAAGATGAGGACATTTTACCTCTAACCCTTGAAGAGAAGGAAAACAAAGAA
TACCTCAAATATCTACTTGAAATCTTGATTCTGATGGGAAGGCAAAACATACCTCTGGACGGACATGAGGCTGATGAAAT
CCCAGAAGGTCTCTTTACTCCAGATAACTTTCAGGCACTACTGGAGTGTCGGATAAATTCTGGTGAAGAGGTTCTGAGAA
AGCGGTTTGAGACAACAGCAGTTAACACGTTGTTTTGTTCAAAAACACAGCAGAGGCAGATGCTAGAGATCTGTGAGAGC
TGTATTCGAGAAGAAACTCTCAGGGAAGTGAGAGACTCACACGTCTTTTCCATTATCACTGACGATGTAGTGGACATAGC
AGGGGAAGAGCACCTACCTGTGTTGGTGAGGTTTGTTGATGAATCTCATAACCTAAGAGAGGAATTTATAGGCTTCCTGC
CTTATGAAGCTGATGCAGAAATTTTGGCTGTGAAATTTCACACTATGATAACTGAGAAGTGGGGATTAAATATGGAGTAT
TGTCGTGGCCAGGCTTACATTGTCTCTAGTGGATTTTCTTCCAAAATGAAAGTTGTTGCTTCTAGACTTTTAGAGAAATA
TCCCCAAGCTATCTACACACTCTGCTCTTTCTGTGCCTTAAATATGTGGTTGGCAAAATCAGTACCTGTTATGGGAGTAT
CTGTTGCATTAGGAACAATCGAGGAAGTTTGTTCTTTTTTCCATCGATCACCACAACTGCTTTTAGAACTTGACAACGTA
ATTTCTGTTCTTTTTCAGAACAGTAAAGAAAGGGGTAAAGAACTGAAGGAAATCTGCCATTCTCAGTGGACAGGGAGGCA
TGATGCTTTTGAAATTTTAGTGGAACTCCTGCAAGCACTTGTTTTATGTTTAGATGGTATAAATAGTGACACAAATATTA
GATGGAATAACTGTATAGCTGGCCGAGCATTTGTACTCTGCAGTGCAGTAACAGATTTTGATTTCATTGTTACTATTGTT
GTTCTTAAAAATGTCCTATCTTTTACAAGAGCCTTTGGGAAAAACCTCCAGGGGCAAACCTCTGATGTCTTCTTTGCAGC
CGGTAGCTTGACTGCAGTACTGCATTCACTCAACGAAGTGATGGAAAATATTGAAGTTTATAATGAATTTTGGTTTGAGG
AAGCCACAAATTTGGCAACCAAACTTGATATTCAAATGAAACTCCCTGGGAAATTCCGCAGAGCTCACCAGGGTAACTTG
GAATCTCAGCTAACCTTTGAGAGTTACTATAAAGAAACCCTAAGTGTCCCAACAGTGGAGCACATTATTCAGGAACTTAA
AGATATATTCTCAGAACAGCACCTCAAAGCTCTTAAATGCTTATCTCTGGTACCCTCAGTCATGGGACAACTCAAATTCA
ATACTTTGGAGGAACACCATGCTGACATGTATAGAAGTGACTTACCCAATCCTGACACGCTGTCAGCTGAGCTTCATTGT
TGGGGAATCAAATGGAAACACAGGGGGAAAGATATAGAGCTTCCGTCCACCATCTATGAAGCCCTCCAACTGCCTGACAT
CAAGTTTTTTCCTAATGTGTATGCATTGCTGAAGGTCCTGTGTATTCTTCTGTGATGAAGGTTGAGAATGAGCGGTATGA
AAATGGATGAAAGCGTCTTAAAGCATATTTGAGGAACACTTTGACAGACCAAAGGTCAAGTAACTTGGCTTTGCTTAACA
TAAATTTTGATATAAAACACGACCTGGATTTAATGGTGGACACATATATTAAACTCTATACAAGTAAGTCAGAGCTTCCT
ACAGATAATTCCGAAACTGTGGAAAATACC

ORF - retro_hsap_4080 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.04 %
Parental protein coverage: 99.47 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalCAAPNCTRKSTQSDLAFFRFPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRTSPYR
C............DLAFF.FPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRT.PYR
RetrocopyCRQLHAEEHAVRLDLAFFSFPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRTGPYR
ParentalTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEE
TVLRDNAIPTIFDL.SHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEE
RetrocopyTVLRDNAIPTIFDLNSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEE
ParentalGEGQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEE
GEGQDEDILPLTLEEKENKEYLK.L.EILILMG.QNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEE
RetrocopyGEGQDEDILPLTLEEKENKEYLKYLLEILILMGRQNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEE
ParentalVLRKRFETTAVNTLFCSKTQQRQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVLVRFVD
VLRKRFETTAVNTLFCSKTQQRQMLEICESCIREETLREVRDSH.FSIITDDVVDIAGEEHLPVLVRFVD
RetrocopyVLRKRFETTAVNTLFCSKTQQRQMLEICESCIREETLREVRDSHVFSIITDDVVDIAGEEHLPVLVRFVD
ParentalESHNLREEFIGFLPYEADAEILAVKFHTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQA
ESHNLREEFIGFLPYEADAEILAVKFHTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQA
RetrocopyESHNLREEFIGFLPYEADAEILAVKFHTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQA
ParentalIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICH
IYTLCS.CALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICH
RetrocopyIYTLCSFCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICH
ParentalSQWTGRHDAFEILVELLQALVLCLDGINSDTNIRWNNYIAGRAFVLCSAVSDFDFIVTIVVLKNVLSFTR
SQWTGRHDAFEILVELLQALVLCLDGINSDTNIRWNN.IAGRAFVLCSAV.DFDFIVTIVVLKNVLSFTR
RetrocopySQWTGRHDAFEILVELLQALVLCLDGINSDTNIRWNNCIAGRAFVLCSAVTDFDFIVTIVVLKNVLSFTR
ParentalAFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRAHQGNL
AFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVY.EFWFEEATNLATKLDIQMKLPGKFRRAHQGNL
RetrocopyAFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVYNEFWFEEATNLATKLDIQMKLPGKFRRAHQGNL
ParentalESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTSEEHHADMYRSDLPN
ESQLT.ESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNT.EEHHADMYRSDLPN
RetrocopyESQLTFESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTLEEHHADMYRSDLPN
ParentalPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCIL-PVMKVENERYENGRKR
PDTLSAELHCW.IKWKHRGKDIELPSTIYEAL.LPDIKFFPNVYALLKVLCIL..VMKVENERYENG.KR
RetrocopyPDTLSAELHCWGIKWKHRGKDIELPSTIYEALQLPDIKFFPNVYALLKVLCIL<SVMKVENERYENG*KR
ParentalLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETVENT
LKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETVENT
RetrocopyLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETVENT

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 .18 RPM 37 .15 RPM
bodymap2_adrenal 0 .31 RPM 51 .36 RPM
bodymap2_brain 0 .12 RPM 27 .00 RPM
bodymap2_breast 0 .12 RPM 48 .33 RPM
bodymap2_colon 0 .15 RPM 32 .23 RPM
bodymap2_heart 0 .17 RPM 22 .21 RPM
bodymap2_kidney 0 .43 RPM 36 .60 RPM
bodymap2_liver 0 .00 RPM 13 .52 RPM
bodymap2_lung 0 .19 RPM 31 .08 RPM
bodymap2_lymph_node 0 .09 RPM 39 .25 RPM
bodymap2_ovary 0 .19 RPM 66 .87 RPM
bodymap2_prostate 0 .19 RPM 37 .50 RPM
bodymap2_skeletal_muscle 0 .02 RPM 19 .81 RPM
bodymap2_testis 0 .28 RPM 46 .15 RPM
bodymap2_thyroid 0 .26 RPM 49 .87 RPM
bodymap2_white_blood_cells 0 .85 RPM 102 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4080 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_4080 retrocopy
EST ID Start End Identity Match Mis-match Score
AA362001 79672855 79673141 97.9 278 3 273

TSS - click to see more details

No TSS is located nearby retro_hsap_4080 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4080 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4080 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2766
Parental genes homology:
Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000244881 retrocopy
retro_acar_167,
Bos taurus ENSBTAG000000316092 retrocopies
retro_btau_1797, retro_btau_780,
Canis familiaris ENSCAFG000000052741 retrocopy
retro_cfam_663,
Equus caballus ENSECAG000000219821 retrocopy
retro_ecab_150,
Homo sapiens ENSG00000137492 1 retrocopy
retro_hsap_4080 ,
Mustela putorius furoENSMPUG000000087841 retrocopy
retro_mputfur_1571,
Pan troglodytes ENSPTRG000000040911 retrocopy
retro_ptro_2766,
Tursiops truncatus ENSTTRG000000132871 retrocopy
retro_ttru_126,

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 = 1.45 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .47 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .22 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .37 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .13 RPM
GBR_HG00099 0 .49 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .31 RPM
GBR_HG00131 0 .69 RPM
GBR_HG00133 0 .46 RPM
GBR_HG00134 0 .63 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .28 RPM
GBR_HG00143 0 .16 RPM
TSI_NA20512 0 .23 RPM
TSI_NA20513 1 .45 RPM
TSI_NA20518 0 .39 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .32 RPM
TSI_NA20765 1 .10 RPM
TSI_NA20771 0 .31 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .20 RPM
YRI_NA18907 0 .49 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .24 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .50 RPM
YRI_NA19213 0 .29 RPM
YRI_NA19214 0 .47 RPM
YRI_NA19223 0 .94 RPM

Indel association:

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





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