RetrogeneDB ID:

retro_hsap_2680

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:98376645..98379411(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000244153
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WWP1
Ensembl ID:ENSG00000123124
Aliases:WWP1, AIP5, Tiul1, hSDRP1
Description:WW domain containing E3 ubiquitin protein ligase 1 [Source:HGNC Symbol;Acc:17004]


Retrocopy-Parental alignment summary:






>retro_hsap_2680
ATGGCCACTGCCTCACCAAAGTCAGATACTACTAATAACCACAGTGGAAGGTTGCAGTTACAGGTAACTGTTTCTAGTGC
CAAACTTAAGAGAAGAAAGAACTGGTTCGGAACAGCAATATATACAGAAGTAGTTGTAGATGAGGAAATTAGGAAAACAG
CAAAATCCAGTAGTTCTTCTAATCTAAAATGGGATGAACAGCTAACTGTAAATGTTACGCCACAGACTACATTGGAATTT
CGAGTTTGGAGTCATCACACTTTAAAAGCAGATGCTTAATTAGGAAATGCAACGACAGATCTGAAACAAGCTCTGTTGAT
ACACAATAGAAAACTGGAAAGAGTGAAAGAACAATTAAAACTTTCCTTAGAAAACAAGAATGGCATAGCACAAACTGGTG
AATTGACAGTTGTGCTTGATGGATTGGTGATTGAGCAAGAAAATATAACAAACTGCAGCTCAACTCCAGCCATAGAAATA
CAGCAAAATGGTGATGCCTTACATGAAAATGGAGAGCCTTCAGCAAGGACAACTGCCAGGTTGGCTATTGAAGGCACGAA
TGGAATAGATAATCATGTACCTACAAGCACTCTAGTCCAAAACTCATGCTGCTCGTATGTAGTTAATGGAGACAACATAC
CTTCATCTCCATCTCAGGTTGCTGCCAGACCCAAAAATACACCAGCCCCAAAACTACTCACATCTGAGCCTGCCGATGAC
ACTGTTAATGGAGAATCATCCTCATTTGCACCAACTGATAATGCTTCTGTCATGGGTATTCCAGTAGTGTCTGAAGAAAA
TGCCTTGTCTCCAAATTGCACTAGTACTACTGTTGAAGATCCTCCAGTTCAAGAAATACTGACTTCCTCAGAAAACAATG
AATGCATTCCTTCTACCAGTGCAGAATTGGGATCTGAATCTAGAAGTATATTAGACCCTGACACCTCTAATTCTGGAAGT
AGTTCTGCTTTTGAAACAGCCAAATCAAGACAGCCAGATGGGTGTATGGATCCAGTATAGCAGGAGTCTGGGAATGCCAA
CACAGAAACCTTGCCATCAGGGTGGGAACAAAGAAAATATCCTCATGGTAGAACCTATTATGTGGATCATAATACTCAAA
CTACCACACGGGAGAGACCACAACCTTTACCTTCAGGTTGGGAAAGAAGAGTTGATGATCGTGGAAGAGCTTATTATGTG
GATCATAACACCAGAAGAACAACATGGCAGCGGCCTACCATGGAATGGGTCAGAAATTTTGAACAGTGGCAATCTCAGCA
GAACCAACCTCAGGGAGCTATGCAACAGTTTAACCAATGATACCTCTATTCAGCTTCAATGTTAGCCGCAGAAAATGACC
CTCATGGACCTTTGCCACCAGGCCGGGAAAAAAGAGTGGATTCAACAGACAGGGTTTACTTTGTGAATCGTAATACAAAA
ACAACCCAGTGGGAAGATCCAAGAACTCAAGGCTTACAGAATGAAGAACCTCTGCCAGAAGGCTGGGAAATAAGATATAC
TCGTGAAGGTGTAAGGTACTTTGTTAATCACAATGCAAGAACAACAACATTCAAAGATCCTTGCAATGGGAAGTCATCCA
TAACTAAAGGTGGTCCACAAATTGATTATGAACACAGCTTTAGGCGGAAACTTGCTCACTTCCGTTATTTGTGCCAGTCT
AATGCACTACCCAGTCATGTAAAGATCAATGTGTCCCGGCAGACATTGTTTGAAGATTCCTTCCAACAGATTATGGCATT
AAAACCTTATGACTTGAGGAGGTGCTTATATGTAATATTTAGAGGAGAAGAAGGACTTGATTATGGTGGCCTAGCAAGAG
AATGGCTTTTCTTGCTTTCACATGAAGTTTTGAACCCAATGTAATGCTTATTTGAGTATGTGGGGAAGAACAACTATTCT
CTGCAGATAAATCCAGCATCAACCATTAATCCAGACCATCTTTCATACTACTGTTTCATTGGTCGTTTTATTGCCATGGC
ACTATTTCATGGAAAGCTTATAGATACTGGTTTCTCTTTACCATTCTACAAGCATATGTTAAGTAAAAAACTTACTATTA
AGGATTTGGAATCTATTGATACTGAATTTTATAACTCCCTTATCTGGATAAGAGATAACAACATTGAAGAATGTGGCTTA
GAACTGTACTTTTCTGTTGACATGGAGAGTTGGGGAAAAGTTACTTCACATGACCTGAAGTTGGGAGTTTCCAATATTCT
GGTGACTGAGGAGAACAAAGATGAATATATTGGTTTAATGACAGAATGGCATTTTTCTCGAGGAGTACAAGAACAGACCA
AAGCTTTCCTTGATGGTTTTAATGGAGTTGTTCCTCATCAGTGGCTACAGTACTTCAATGAAAAAGAATTAGAGGTTACG
TTGTGTGGCACACAGCAGGTTGACTTGGCAGATTGGCAGAGAAATACTGTTTATCAACATTATACAAGAAACAGCAAGCA
AATCATTCGGTTCTGGCAGTTTGTGAAAGAGACAGACAATGAAGTAAGAATGCTACTATTGCAGTTCGTCACTGGAACCT
GCCGTTTATCTCTAGGAGGATTTGCTGAGCTCATGGGAAGTAATGGGCCTCAAAAGTTTTGCATTGAAAAAGTTGGCAAA
GATACTTGGTTACCAAGAAGCCATACATGTTTTAATCTCTTGGATCTACCACCATATAAGAGTTATGAACAACTAAAGGA
AAAACTTCTTTTTGCAATAGAAGAGACAGAGGGATGTGGACAAGAA

ORF - retro_hsap_2680 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.97 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATASPRSDTSNNHSGRLQLQVTVSSAKLKRKKNWFGTAIYTEVVVDGEITKTAKSSSSSNPKWDEQLTV
MATASP.SDT.NNHSGRLQLQVTVSSAKLKR.KNWFGTAIYTEVVVD.EI.KTAKSSSSSN.KWDEQLTV
RetrocopyMATASPKSDTTNNHSGRLQLQVTVSSAKLKRRKNWFGTAIYTEVVVDEEIRKTAKSSSSSNLKWDEQLTV
ParentalNVTPQTTLEFQVWSHRTLKADALLGKATIDLKQALLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLD
NVTPQTTLEF.VWSH.TLKADA.LG.AT.DLKQALLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLD
RetrocopyNVTPQTTLEFRVWSHHTLKADA*LGNATTDLKQALLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLD
ParentalGLVIEQENITNCSSSPTIEIQENGDALHENGEPSARTTARLAVEGTNGIDNHVPTSTLVQNSCCSYVVNG
GLVIEQENITNCSS.P.IEIQ.NGDALHENGEPSARTTARLA.EGTNGIDNHVPTSTLVQNSCCSYVVNG
RetrocopyGLVIEQENITNCSSTPAIEIQQNGDALHENGEPSARTTARLAIEGTNGIDNHVPTSTLVQNSCCSYVVNG
ParentalDNTPSSPSQVAARPKNTPAPKPLASEPADDTVNGESSSFAPTDNASVTGTPVVSEENALSPNCTSTTVED
DN.PSSPSQVAARPKNTPAPK.L.SEPADDTVNGESSSFAPTDNASV.G.PVVSEENALSPNCTSTTVED
RetrocopyDNIPSSPSQVAARPKNTPAPKLLTSEPADDTVNGESSSFAPTDNASVMGIPVVSEENALSPNCTSTTVED
ParentalPPVQEILTSSENNECIPSTSAELESEARSILEPDTSNSRSSSAFEAAKSRQPDGCMDPVRQQSGNANTET
PPVQEILTSSENNECIPSTSAEL.SE.RSIL.PDTSNS.SSSAFE.AKSRQPDGCMDPV.Q.SGNANTET
RetrocopyPPVQEILTSSENNECIPSTSAELGSESRSILDPDTSNSGSSSAFETAKSRQPDGCMDPV*QESGNANTET
ParentalLPSGWEQRKDPHGRTYYVDHNTRTTTWERPQPLPPGWERRVDDRRRVYYVDHNTRTTTWQRPTMESVRNF
LPSGWEQRK.PHGRTYYVDHNT.TTT.ERPQPLP.GWERRVDDR.R.YYVDHNTR.TTWQRPTME.VRNF
RetrocopyLPSGWEQRKYPHGRTYYVDHNTQTTTRERPQPLPSGWERRVDDRGRAYYVDHNTRRTTWQRPTMEWVRNF
ParentalEQWQSQRNQLQGAMQQFNQRYLYSASMLAAENDPYGPLPPGWEKRVDSTDRVYFVNHNTKTTQWEDPRTQ
EQWQSQ.NQ.QGAMQQFNQ.YLYSASMLAAENDP.GPLPPG.EKRVDSTDRVYFVN.NTKTTQWEDPRTQ
RetrocopyEQWQSQQNQPQGAMQQFNQ*YLYSASMLAAENDPHGPLPPGREKRVDSTDRVYFVNRNTKTTQWEDPRTQ
ParentalGLQNEEPLPEGWEIRYTREGVRYFVDHNTRTTTFKDPRNGKSSVTKGGPQIAYERGFRWKLAHFRYLCQS
GLQNEEPLPEGWEIRYTREGVRYFV.HN.RTTTFKDP.NGKSS.TKGGPQI.YE..FR.KLAHFRYLCQS
RetrocopyGLQNEEPLPEGWEIRYTREGVRYFVNHNARTTTFKDPCNGKSSITKGGPQIDYEHSFRRKLAHFRYLCQS
ParentalNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCL
NALPSHVKINVSRQTLFEDSFQQIMALKPYDLRR.LYVIFRGEEGLDYGGLAREW.FLLSHEVLNPM.CL
RetrocopyNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRCLYVIFRGEEGLDYGGLAREWLFLLSHEVLNPM*CL
ParentalFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESID
FEY.GKNNY.LQINPASTINPDHLSY.CFIGRFIAMALFHGK.IDTGFSLPFYK.MLSKKLTIKDLESID
RetrocopyFEYVGKNNYSLQINPASTINPDHLSYYCFIGRFIAMALFHGKLIDTGFSLPFYKHMLSKKLTIKDLESID
ParentalTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQ
TEFYNSLIWIRDNNIEECGLE.YFSVDME..GKVTSHDLKLG.SNILVTEENKDEYIGLMTEW.FSRGVQ
RetrocopyTEFYNSLIWIRDNNIEECGLELYFSVDMESWGKVTSHDLKLGVSNILVTEENKDEYIGLMTEWHFSRGVQ
ParentalEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDN
EQTKAFLDGFN.VVP.QWLQYF.EKELEV.LCG.Q.VDLADWQRNTVY.HYTRNSKQII.FWQFVKETDN
RetrocopyEQTKAFLDGFNGVVPHQWLQYFNEKELEVTLCGTQQVDLADWQRNTVYQHYTRNSKQIIRFWQFVKETDN
ParentalEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNRLDLPPYKSYEQLKEKLL
EVRM.LLQFVTGTCRL.LGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFN.LDLPPYKSYEQLKEKLL
RetrocopyEVRMLLLQFVTGTCRLSLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNLLDLPPYKSYEQLKEKLL
ParentalFAIEETEGFGQE
FAIEETEG.GQE
RetrocopyFAIEETEGCGQE

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 84 .16 RPM
bodymap2_adrenal 0 .02 RPM 69 .02 RPM
bodymap2_brain 0 .00 RPM 44 .04 RPM
bodymap2_breast 0 .04 RPM 102 .04 RPM
bodymap2_colon 0 .00 RPM 95 .75 RPM
bodymap2_heart 0 .06 RPM 191 .53 RPM
bodymap2_kidney 0 .10 RPM 97 .12 RPM
bodymap2_liver 0 .02 RPM 96 .51 RPM
bodymap2_lung 0 .00 RPM 74 .02 RPM
bodymap2_lymph_node 0 .15 RPM 75 .73 RPM
bodymap2_ovary 0 .00 RPM 53 .96 RPM
bodymap2_prostate 0 .03 RPM 95 .50 RPM
bodymap2_skeletal_muscle 0 .00 RPM 113 .73 RPM
bodymap2_testis 0 .00 RPM 92 .34 RPM
bodymap2_thyroid 0 .02 RPM 94 .19 RPM
bodymap2_white_blood_cells 0 .02 RPM 86 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2680 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2680 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2680 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2680 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2680 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1807
Pongo abelii retro_pabe_2299
Macaca mulatta retro_mmul_1418
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000123124 1 retrocopy
retro_hsap_2680 ,
Macaca mulatta ENSMMUG000000063051 retrocopy
retro_mmul_1418,
Mustela putorius furoENSMPUG000000108071 retrocopy
retro_mputfur_963,
Mus musculus ENSMUSG000000410581 retrocopy
retro_mmus_2017,
Nomascus leucogenys ENSNLEG000000015171 retrocopy
retro_nleu_1183,
Pongo abelii ENSPPYG000000187241 retrocopy
retro_pabe_2299,
Pan troglodytes ENSPTRG000000203951 retrocopy
retro_ptro_1807,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 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 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017