RetrogeneDB ID:

retro_hsap_463

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:166244868..166246129(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215835
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EWSR1
Ensembl ID:ENSG00000182944
Aliases:EWSR1, EWS, bK984G1.4
Description:EWS RNA-binding protein 1 [Source:HGNC Symbol;Acc:3508]


Retrocopy-Parental alignment summary:






>retro_hsap_463
CCTCCCACTAGTTACCCACCCCAAACTTGATCCTACAGCCAAGCTCCAAGTCAGTATAGCTAACAGAGCAGCAGCTACGG
GCAGCAGAGTTCATTCTGACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCGGACTAG
GAGAGAACCGGAGCATGAGTGGCCCTGATAACTGGGGCAGGGGAAGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGGT
GGGCGGGGAGGAGGATGCGGTGGAATGGGCAGCGCTGGAGAGCAAGTTGGCTTCAATAAGCCTGGTGGACCCATGGATGA
AGGACCAGATCTTGATCTAGGCCCACCTGTAGATCCAGATGAAGACTCTGACAACAGTGCAATTTATGTACAAGGATTAA
ATGACAATGTGACTCTAGATGATCTGGTAGACTTCTTTAAGCAGTGTGGGGTTGTTAAGATGAACAAGAGAACTGAGCAA
CCCATGATCCACACCTACCTGGACAAGGAAACAAGAAAGCCCAAAGGTGATGCCACAGTGTCCTGTGAAGACTCACCTAC
TGCCAAAGCTGCCGTGGAATGGTTTGATGGGAAAGATTTTCAAGGGAGCAAACTTAAAGTCTCTCTTGCTCGGAAGAGGC
CTCCAGTGAACAGTATGCAGGGTGGTATGCCACCCCATGAGGGCAGAGGGATGCCACCACCACTCTGCGGAGGTCCAGGA
GGCCCAGGAAGTCCTGGGGGACCCATGGGTCACATGGGAGGCCGTGGAGGAGATAGAGGAGGCCTCCCTCCAAGAGGACC
CCAGGGTTCCCGAGGGAACACCTCTGGAGGAGGAAACGTCCAGCACCAAGCTGGAGACAGGCAGTGTCCCAATCCGGGTT
GTGGAAACCAGAACTTCGCCTGGAGAACAGAGAGCAACAAGTGTAAGGCTCCAAAGCCTGAAGGCTTCCTCCCGCCACCC
TTCCCACCCCCGGGTGGTGATCATGGCAGAGGTGGCCCTGGTGGCATGTGGGGAGGAAGAGGTGGCCTCATGGATCATGG
TGGTCCCGGTGGAATGTTCAGAGGTGGCTGTGGTAGAGACAGAAGTGGCTTCTGTGGTGGCTGGGCATGGACCGAGGTGG
CTTTGGTGGAGGAAGACAAGGTGGCCCTGGGGGGCCCCCGGACCTTTGATGTAACCAATGGGAGGAAGAAGAGGAGGACG
TGAAGGACCTGGAAAAACGGATAAAGGCGAGCACTGTCAGGAGCGCAGAGATCAGCCCTAC

ORF - retro_hsap_463 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.89 %
Parental protein coverage: 70.17 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRG
PPTSYPPQT.SYSQAPSQYS.QSSSYGQQSSF.QDHPSSMGVYGQESGGFSG.GENRSMSGPDN.GRGRG
RetrocopyPPTSYPPQT*SYSQAPSQYS*QSSSYGQQSSF*QDHPSSMGVYGQESGGFSGLGENRSMSGPDNWGRGRG
ParentalGFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDSVTLD
GFDRGGMSRGGRGGG.GGMGSAGE..GFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLND.VTLD
RetrocopyGFDRGGMSRGGRGGGCGGMGSAGEQVGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDNVTLD
ParentalDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA
DL.DFFKQCGVVKMNKRT.QPMIH.YLDKET.KPKGDATVS.ED.PTAKAAVEWFDGKDFQGSKLKVSLA
RetrocopyDLVDFFKQCGVVKMNKRTEQPMIHTYLDKETRKPKGDATVSCEDSPTAKAAVEWFDGKDFQGSKLKVSLA
ParentalRKKPPMNSMRGGLPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNV
RK.PP.NSM.GG.PP.EGRGMPPPL.GGPGGPG.PGGPMG.MGGRGGDRGG.PPRGP.GSRGN.SGGGNV
RetrocopyRKRPPVNSMQGGMPPHEGRGMPPPLCGGPGGPGSPGGPMGHMGGRGGDRGGLPPRGPQGSRGNTSGGGNV
ParentalQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGPG
QH.AGD.QCPNPGCGNQNFAWRTE.N.CKAPKPEGFLPPPFPPPGGD.GRGGPGGM.GGRGGLMD.GGPG
RetrocopyQHQAGDRQCPNPGCGNQNFAWRTESNKCKAPKPEGFLPPPFPPPGGDHGRGGPGGMWGGRGGLMDHGGPG
ParentalGMFRGGRGGDRGGFRGG-RGMDRGGFGGGRRGGPGGPP-GPLMEQMGGRRGGRGGPGKMDKGEHRQERRD
GMFRGG.G.DR.GF.GG..GMDRGGFGGGR.GGPGGPP.GPLM..MGGRRGGR.GPGK.DKGEH.QERRD
RetrocopyGMFRGGCGRDRSGFCGG<LGMDRGGFGGGRQGGPGGPP<GPLM*PMGGRRGGREGPGKTDKGEHCQERRD
ParentalRPY
.PY
RetrocopyQPY

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 137 .18 RPM
bodymap2_adrenal 0 .10 RPM 298 .49 RPM
bodymap2_brain 0 .02 RPM 146 .76 RPM
bodymap2_breast 0 .00 RPM 124 .55 RPM
bodymap2_colon 0 .00 RPM 69 .32 RPM
bodymap2_heart 0 .00 RPM 88 .28 RPM
bodymap2_kidney 0 .04 RPM 117 .90 RPM
bodymap2_liver 0 .00 RPM 72 .88 RPM
bodymap2_lung 0 .00 RPM 96 .75 RPM
bodymap2_lymph_node 0 .00 RPM 144 .25 RPM
bodymap2_ovary 0 .04 RPM 149 .34 RPM
bodymap2_prostate 0 .02 RPM 132 .19 RPM
bodymap2_skeletal_muscle 0 .02 RPM 99 .69 RPM
bodymap2_testis 0 .11 RPM 179 .84 RPM
bodymap2_thyroid 0 .00 RPM 202 .19 RPM
bodymap2_white_blood_cells 0 .08 RPM 144 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_463 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_463 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_463 retrocopy 5' end.

Lab - click to see more details

retro_hsap_463 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_463 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_350
Gorilla gorilla retro_ggor_444
Parental genes homology:
Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000082982 retrocopies
retro_amel_191, retro_amel_959,
Canis familiaris ENSCAFG000000121608 retrocopies
retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus ENSCJAG000000199874 retrocopies
retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Homo sapiens ENSG00000182944 1 retrocopy
retro_hsap_463 ,
Gorilla gorilla ENSGGOG000000122121 retrocopy
retro_ggor_444,
Macropus eugenii ENSMEUG000000087031 retrocopy
retro_meug_1424,
Myotis lucifugus ENSMLUG000000120581 retrocopy
retro_mluc_328,
Monodelphis domestica ENSMODG000000086791 retrocopy
retro_mdom_279,
Oryctolagus cuniculus ENSOCUG000000044322 retrocopies
retro_ocun_1346, retro_ocun_242,
Pongo abelii ENSPPYG000000116841 retrocopy
retro_pabe_1769,
Pan troglodytes ENSPTRG000000142181 retrocopy
retro_ptro_350,
Ictidomys tridecemlineatus ENSSTOG000000231771 retrocopy
retro_itri_1892,
Tursiops truncatus ENSTTRG000000118811 retrocopy
retro_ttru_1366,

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 = 0.53 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .23 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .19 RPM
FIN_HG00183 0 .25 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .22 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .26 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .44 RPM
FIN_HG00377 0 .53 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .21 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .22 RPM
GBR_HG00134 0 .26 RPM
GBR_HG00137 0 .22 RPM
GBR_HG00142 0 .22 RPM
GBR_HG00143 0 .16 RPM
TSI_NA20512 0 .28 RPM
TSI_NA20513 0 .22 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .37 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .23 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .20 RPM
TSI_NA20786 0 .29 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .28 RPM
YRI_NA18916 0 .38 RPM
YRI_NA19093 0 .31 RPM
YRI_NA19099 0 .32 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 0 .23 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .12 RPM

Indel association:

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





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