RetrogeneDB ID:

retro_hsap_891

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:71960893..71962332(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228286
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DOK1
Ensembl ID:ENSG00000115325
Aliases:DOK1, P62DOK
Description:docking protein 1, 62kDa (downstream of tyrosine kinase 1) [Source:HGNC Symbol;Acc:2990]


Retrocopy-Parental alignment summary:






>retro_hsap_891
ATGGACGGAGCTATGACAGAAGGGCCGCTCTTTTCGCAGAGTCAGCACTTTGGGACCAAGAGGTGGAGGAAGACCTGGGC
CATGCTCTACCCGGCCAGTCCCCATGGCTAGCGCGGCTCAAGTTCTTTGACCATAAGGGGTCGAGCTCTGGGAGTGGCCG
AGGGAGCTCGTGCTGCCTGGACTGCAAGGTGATCCATCTGGCGAAGTGTGTGAGTTTGGTCCCCGTGGCCGTGGAGAGCC
TCCCTGAGCCCAGCGCCACTGCCTTCCGCCTGGACACTGCACAGCACTAGCACCTGCTGGCTGTTGATGTGCCGTCCAGT
GCAGCCTGGTTGCAGACGCTGTGCCAAAACCCCCTTCGGAAAGGCAGCTGGACTCTGGAACCTACCAATAACCCACCTGA
GCTTTCTGCCCTGGAGATGCTGGAGAACTCCTTGTGCAGCCCCACCTGGGAAGGATCCCAGTTCTGGGTAACGGTGCAGA
GGACTGAGGCGGTCGAGCACTGTGGCCTGCATGCCTCCTACGTGCTGAGGGTGGAGGCTGAAAGGCTGACTCTCCTGACC
ATGGGAGCCCAGAGTCAGGTACCGGAGCTGCTCCTGTCCTGGCCCTACACTCTGTTGCATTGCTATGGCCGGGACAAGGT
CATGTTCTCTTTTGAGGCCAGCGCCGCTGCCTCTTGGGCCCTGGAACCTTCCTTTCCAGACGGCACAGGGAAATGACATC
TTCCAGGCAGATGAGACTGCCATCCACCGGCAGAAGGCCCAGGGAAAGGCCAGACAGGGGCACAATGCTCTCAGAGCTGA
TTCCCATGAAAGGAAGGTGGTAGAGGGGAAGTTCTCTTCCCCACCTGGACCCCAAGAGCTCCTTGAAAGCCCCCCAGCCC
TGTATGCTGAGCCCTTAGACTCCCTGCACATTGCTTCAGGCCCATCCCAGGGCTCCCTATACTCAGACCTCTTGGACGGC
ACTCTTGCTCGGGCAGGAGAGGGAGTACAATGGAAGAAACCTCTCTATTGGGACTTGTATGAGCATGAGCAGCAGCAGTT
GCTGAAGGCCAAGCTGACGGACCCCAAAGAGGATCCCATCTATGATGAACCCGAGGGCCTGGCCCCAGCCCTTCCCCAGG
GCCTTTATGATCTGCCTTAGGAGCCCAAAGATGTGTGGGATGTCAAGCTGAGGTGAAGTAGGAGGGCTACAAGCTCCCCT
ACAACCCTGCCACTGATGACTACGCTATGCCACCCACCCAGAGAACAAAGACCCTCCCTGCTTCCAAGTCCCAGGGCCCA
GCCTTCCCTGAACCTAGTACTGCAACTGGCAGGAGCAGCAAAAGCCACAACTCAGCCCTGTACAGCCAGGTCCAGAAGAG
TGGAGCCTCAGGGAGCAGGGACTGTGTGCTTTCTACAGTAGGGACTGACAGGACTGGGGTCAAGTCAGAGGTCTCTACC

ORF - retro_hsap_891 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMDGAVMEGPLFLQSQRFGTKRWRKTWAVLYPASPHG-VARLEFFDHKGSSSGGGRGSSRRLDCKVIRLAE
MDGA..EGPLF.QSQ.FGTKRWRKTWA.LYPASPHG..ARL.FFDHKGSSSG.GRGSS..LDCKVI.LA.
RetrocopyMDGAMTEGPLFSQSQHFGTKRWRKTWAMLYPASPHG<LARLKFFDHKGSSSGSGRGSSCCLDCKVIHLAK
ParentalCVSVAPVTVETPPEPGATAFRLDTAQRSHLLAADAPSSAAWVQTLCRNAFPKGSWTLAPTDNPPKLSALE
CVS..PV.VE..PEP.ATAFRLDTAQ..HLLA.D.PSSAAW.QTLC.N...KGSWTL.PT.NPP.LSALE
RetrocopyCVSLVPVAVESLPEPSATAFRLDTAQH*HLLAVDVPSSAAWLQTLCQNPLRKGSWTLEPTNNPPELSALE
ParentalMLENSLYSPTWEGSQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRY
MLENSL.SPTWEGSQFWVTVQRTEA.E.CGLH.SYVLRVEAERLTLLT.GAQSQ..E.LLSWPYTLL..Y
RetrocopyMLENSLCSPTWEGSQFWVTVQRTEAVEHCGLHASYVLRVEAERLTLLTMGAQSQVPELLLSWPYTLLHCY
ParentalGRDKVMFSFEAG-RRCPSGPGTF-TFQTAQGNDIFQAVETAIHRQKAQGKAGQGHDVLRADSHEGEVAEG
GRDKVMFSFEA..RRC..GPGTF..FQTAQGNDIFQA.ETAIHRQKAQGKA.QGH..LRADSHE..V.EG
RetrocopyGRDKVMFSFEAS<RRCLLGPGTF<PFQTAQGNDIFQADETAIHRQKAQGKARQGHNALRADSHERKVVEG
ParentalKLPSPPGPQELLDSPPALYAEPLDSLRIAPCPSQDSLYSDPLDSTSAQAGEGVQRKKPLYWDLYEHAQQQ
K..SPPGPQELL.SPPALYAEPLDSL.IA..PSQ.SLYSD.LD.T.A.AGEGVQ.KKPLYWDLYEH.QQQ
RetrocopyKFSSPPGPQELLESPPALYAEPLDSLHIASGPSQGSLYSDLLDGTLARAGEGVQWKKPLYWDLYEHEQQQ
ParentalLLKAKLTDPKEDPIYDEPEGLAPVPPQGLYDLPREPKDAW-WCQARVKEEGYELPYNPATDDYAVPPPRS
LLKAKLTDPKEDPIYDEPEGLAP..PQGLYDLP.EPKD.W..CQA.VK.EGY.LPYNPATDDYA.PP...
RetrocopyLLKAKLTDPKEDPIYDEPEGLAPALPQGLYDLP*EPKDVW<GCQAEVK*EGYKLPYNPATDDYAMPPTQR
ParentalTKPLLAPKPQGPAFPEPGTATGSGIKSHNSALYSQVQKSGASGSWDCGLSRVGTDKTGVKSEGST
TK.L.A.K.QGPAFPEP.TATG...KSHNSALYSQVQKSGASGS.DC.LS.VGTD.TGVKSE.ST
RetrocopyTKTLPASKSQGPAFPEPSTATGRSSKSHNSALYSQVQKSGASGSRDCVLSTVGTDRTGVKSEVST

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 10 .75 RPM
bodymap2_adrenal 0 .02 RPM 11 .63 RPM
bodymap2_brain 0 .02 RPM 2 .81 RPM
bodymap2_breast 0 .00 RPM 30 .12 RPM
bodymap2_colon 0 .00 RPM 8 .37 RPM
bodymap2_heart 0 .00 RPM 1 .81 RPM
bodymap2_kidney 0 .08 RPM 4 .57 RPM
bodymap2_liver 0 .00 RPM 1 .04 RPM
bodymap2_lung 0 .00 RPM 7 .65 RPM
bodymap2_lymph_node 0 .00 RPM 17 .12 RPM
bodymap2_ovary 0 .00 RPM 8 .85 RPM
bodymap2_prostate 0 .00 RPM 7 .15 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .38 RPM
bodymap2_testis 0 .04 RPM 6 .03 RPM
bodymap2_thyroid 0 .02 RPM 5 .16 RPM
bodymap2_white_blood_cells 0 .00 RPM 32 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_891 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_891 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_891 retrocopy 5' end.

Lab - click to see more details

retro_hsap_891 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_891 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_615
Macaca mulatta retro_mmul_1103
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000115325 1 retrocopy
retro_hsap_891 ,
Macaca mulatta ENSMMUG000000021391 retrocopy
retro_mmul_1103,
Nomascus leucogenys ENSNLEG000000010101 retrocopy
retro_nleu_391,
Pongo abelii ENSPPYG000000122641 retrocopy
retro_pabe_767,
Pan troglodytes ENSPTRG000000121001 retrocopy
retro_ptro_615,

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 .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 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 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 .00 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).





Copyright © RetrogeneDB 2014-2017