RetrogeneDB ID:

retro_hsap_1543

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:29525886..29527341(-)
Located in intron of:ENSG00000104059
Retrocopy
information
Ensembl ID:ENSG00000259299
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DCAF6
Ensembl ID:ENSG00000143164
Aliases:DCAF6, 1200006M05Rik, ARCAP, IQWD1, MSTP055, NRIP, PC326
Description:DDB1 and CUL4 associated factor 6 [Source:HGNC Symbol;Acc:30002]


Retrocopy-Parental alignment summary:






>retro_hsap_1543
ATGTCTCGGGGTGGCTCCTGCCCACATCTGTTGTGGGACATGAGGAAAAGGTCCCTCGGGCTGGAGGACCTGTCCTGGCT
GTGGGGCCACTACCTGGGAAGAAGAGAATTTATCTAAAGATTGAAACTTCAAGCAACCCTAAATGTGCATGATGGCTGTG
TTAATACAATCTGTTGGAATGACACTGGAGAATATATTTTATCTGGCTCAGATGACACCAAATTAGTAATTAGTAATCCC
TACAGCAGAAAGGTTTTGACAACAATTCGTTCGGGGCACCAAGCAAACATATCTAATGCAAAGTTCTTACCTTGCACAAA
TGATAAACAGATTGTATCCTGCTCTGGAGATGGAGTAATATTTTATACCAATGTTGAGCAAGATGCAGAAACCAACAGAC
AATGCCAATTTACTTGCCACAATGGAACTACTTATGAGATTATGACTGTACCCAATGACCCTTACACTTTTCTCTCTTGT
GGTGAAGATAGAACTGGTAGGTGGTTTGATACACGCATCAAAACTAGCTGCACAAAAGAAGATTGTGAAGATGATATTTT
AATTAGCTGTCGACGTGCTGCCACATCTGTTGCTATTTGCCCACCAATACCATATTACCTTGCCGTTGGTTGTTCTTATA
GCTCAGTACAAATATATGATAGGCGAATGCTGGGCACAAGAGCTACAGGGAATTATGCAGGTCGAGGGACTACTGGAATG
GTTGCCCATTTTATTGCTTCCCATCTTAATAATAAGTCCTGCAGAGTGACATTTCTGTGTTACAGTGAAGATGGTCAAGA
GATTCTCATTAGTTACTCTTCAGATTACATATATCTTTTTGACCCGAAAGATGATACAGCACGAGAACTTAAAACTCCTT
CTGCGGAAGAGAGAAGAGAAGAGTTACGACAACCACCAGTTAAGCGTTTGAGCCTTCGTGGTGATTGGTCAGATACTGGA
CCCAGATCAAGGCCTGAGAGTGAACGAGAATGACATGGAGAGCAGAGTCCCAATGTGTCATTGATGCAGAGAATGTCTGA
TATGTTATCAAGACGGTTCGAAGAAGCAAGTGAGGTTGCACAAAGCAATAGAGGATGAGGAAGATCTTGACCCAGAGGTG
GAACAAGTCAATCAGATATTTCAACTCTTCCTATGGTCCCATCAAGTCCTGATTTGGAAGTGAGTGAAACTGCAATGGAA
GTAGATACTCCAGCTGAACAGTTTCTTCAGCCATCTACATCCTCTACAATGTCAGCTCAGGCTCATTTGACATCATCTCC
CACAGAAAGCCCTCATTCTACTCCTTTTTAATCTTCGCCAGACAGTGAACAAAGGCAGTCTGTTGAGGCATCTGGACACC
ACACACATCATCAGACTGATTCACCTTCTTCTGTGGTTAACAAACAGCTCAGATCCATGTAACTTGATGAGCAACAGAGT
GCGTGCAACAGGAGA

ORF - retro_hsap_1543 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.42 %
Parental protein coverage: 55.11 %
Number of stop codons detected: 6
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSRGGSYPHLLWDVRKRSLGLEDPSRLRSRYLGRREFIQRLKLEATLNVHDGCVNTICWNDTGEYILSGS
MSRGGS.PHLLWD.RKRSLGLED.S.L...YLGRREFI.RLKL.ATLNVHDGCVNTICWNDTGEYILSGS
RetrocopyMSRGGSCPHLLWDMRKRSLGLEDLSWLWGHYLGRREFI*RLKLQATLNVHDGCVNTICWNDTGEYILSGS
ParentalDDTKLVISNPYSRKVLTTIRSGHRANIFSAKFLPCTNDKQIVSCSGDGVIFYTNVEQDAETNRQCQFTCH
DDTKLVISNPYSRKVLTTIRSGH.ANI..AKFLPCTNDKQIVSCSGDGVIFYTNVEQDAETNRQCQFTCH
RetrocopyDDTKLVISNPYSRKVLTTIRSGHQANISNAKFLPCTNDKQIVSCSGDGVIFYTNVEQDAETNRQCQFTCH
ParentalYGTTYEIMTVPNDPYTFLSCGEDGTVRWFDTRIKTSCTKEDCKDDILINCRRAATSVAICPPIPYYLAVG
.GTTYEIMTVPNDPYTFLSCGED.T.RWFDTRIKTSCTKEDC.DDILI.CRRAATSVAICPPIPYYLAVG
RetrocopyNGTTYEIMTVPNDPYTFLSCGEDRTGRWFDTRIKTSCTKEDCEDDILISCRRAATSVAICPPIPYYLAVG
ParentalCSDSSVRIYDRRMLGTRATGNYAGRGTTGMVARFIPSHLNNKSCRVTSLCYSEDGQEILVSYSSDYIYLF
CS.SSV.IYDRRMLGTRATGNYAGRGTTGMVA.FI.SHLNNKSCRVT.LCYSEDGQEIL.SYSSDYIYLF
RetrocopyCSYSSVQIYDRRMLGTRATGNYAGRGTTGMVAHFIASHLNNKSCRVTFLCYSEDGQEILISYSSDYIYLF
ParentalDPKDDTARELKTPSAEERREELRQPPVKRLRLRGDWSDTGPRARPESERERDGEQSPNVSLMQRMSDMLS
DPKDDTARELKTPSAEERREELRQPPVKRL.LRGDWSDTGPR.RPESERE..GEQSPNVSLMQRMSDMLS
RetrocopyDPKDDTARELKTPSAEERREELRQPPVKRLSLRGDWSDTGPRSRPESERE*HGEQSPNVSLMQRMSDMLS
ParentalRWFEEASEVAQSNRGRGRSRPRGGTSQSDISTLPTVPSSPDLEVSETAMEVDTPAEQFLQPSTSSTMSAQ
R.FEEASEVAQSNRG.GRS.PRGGTSQS....................MEVDTPAEQFLQPSTSSTMSAQ
RetrocopyRRFEEASEVAQSNRG*GRS*PRGGTSQSXXXXXXXXXXXXXXXXXXXXMEVDTPAEQFLQPSTSSTMSAQ
ParentalAHSTSSPTESPHSTPLLSSPDSEQRQSVEASGHHTHHQSDSPSSVVNKQLGSMSLDEQQDNNNEK
AH.TSSPTESPHSTP..SSPDSEQRQSVEASGHHTHHQ.DSPSSVVNKQL.SM.LDEQQ...N..
RetrocopyAHLTSSPTESPHSTPF*SSPDSEQRQSVEASGHHTHHQTDSPSSVVNKQLRSM*LDEQQSACNRR

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 60 .35 RPM
bodymap2_adrenal 0 .00 RPM 40 .26 RPM
bodymap2_brain 0 .02 RPM 82 .51 RPM
bodymap2_breast 0 .00 RPM 115 .72 RPM
bodymap2_colon 0 .00 RPM 88 .62 RPM
bodymap2_heart 0 .00 RPM 291 .80 RPM
bodymap2_kidney 0 .08 RPM 68 .84 RPM
bodymap2_liver 0 .00 RPM 74 .29 RPM
bodymap2_lung 0 .00 RPM 50 .14 RPM
bodymap2_lymph_node 0 .00 RPM 54 .07 RPM
bodymap2_ovary 0 .00 RPM 64 .19 RPM
bodymap2_prostate 0 .00 RPM 88 .23 RPM
bodymap2_skeletal_muscle 0 .04 RPM 556 .95 RPM
bodymap2_testis 0 .00 RPM 181 .57 RPM
bodymap2_thyroid 0 .00 RPM 161 .35 RPM
bodymap2_white_blood_cells 0 .00 RPM 35 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1543 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1543 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1543 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1543 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1543 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000143164 1 retrocopy
retro_hsap_1543 ,
Oryctolagus cuniculus ENSOCUG000000044702 retrocopies
retro_ocun_1354, retro_ocun_802,

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 = 0.07 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 .05 RPM
CEU_NA12760 0 .00 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 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .03 RPM
GBR_HG00143 0 .03 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 .06 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 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).





Copyright © RetrogeneDB 2014-2017