RetrogeneDB ID:

retro_hsap_11

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:122133382..122134375(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000196981
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR5
Ensembl ID:ENSG00000196363
Aliases:WDR5, BIG-3, SWD3
Description:WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]


Retrocopy-Parental alignment summary:






>retro_hsap_11
ATGGCAACCAAGGAGTCAAGAGACGCCAAAGCACAGTTGGCCCTCTCCTCATCGGCCAATCAGAGCAAGGAAGTGCCTGA
AAACCCAAACTATGCTCTCAAATGTACTCTTGTGGGACACACGGAAGCAGTGTCATCAGTTAAGTTTAGTCCTAATGGAG
AATGGCTAGCAAGTTCTTCTGCTGATAGGCTAATCATAATTTGGGGAGCATATGATGGAAAATATGAGAAAACACTCTAT
GGTCATAATTTGGAAATATCGGATGTTGCCTGGTCATCAGATTCCAGTCGTCTTGTTTCTGCCTCAGATGATAAAACTCT
AAAATTATGGGATGTGAGATCTGGAAAATGTTTGAAAACACTGAAGGGGCACAGTAATTATGTCTTTTGTTGTAACTTCA
ATCCGCCATCCAACCTTATAATCTCGGGATCTTTTGATGAGACTGTAAAAATATGGGAGGTGAAAACAGGAAAGTGTCTC
AAGACTTTGTCTGCTCATTCTGACCCAGTTTCTGCTGTTCATTTTAATTGTAGTGGGTCCTTGATAGTGTCAGGTAGCTA
TGATGGCCTCTGTAGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAAACGCTCGTTGATGACGATAACCCTCCTGTCT
CTTTTGTAAAATTTTCTCCAAATGGTAAATACATTCTCACTGCAACTTTGGACAACACTCTTAAACTATGGGATTATAGC
AGAGGCAGGTGCCTGAAAACATACACTGGTCATAAGAATGAGAAATATTGCATATTTGCCAATTTTTCAGTTACTGGTGG
AAAGTGGATTGTGTCTGGTTCCGAGGATAACCTGGTTTACATTTGGAACCTTCAGACTAAAGAGATTGTGCAGAAATTAC
AAGGCCATACAGATGTTGTGATCTCAGCAGCTTGTCATCCTACAGAAAACCTCATCGCATCAGCAGCATTAGAAAATGAC
AAAACAATTAAACTGTGGATGAGTAACCACTAA

ORF - retro_hsap_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.46 %
Parental protein coverage: 97.31 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGK
E...A.AQ...SSSA.QSK..P..PNYALK.TL.GHT.AVSSVKFSPNGEWLASSSAD.LI.IWGAYDGK
RetrocopyESRDAKAQLALSSSANQSKEVPENPNYALKCTLVGHTEAVSSVKFSPNGEWLASSSADRLIIIWGAYDGK
ParentalFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGS
.EKT..GH.L.ISDVAWSSDS..LVSASDDKTLK.WDV.SGKCLKTLKGHSNYVFCCNFNP.SNLI.SGS
RetrocopyYEKTLYGHNLEISDVAWSSDSSRLVSASDDKTLKLWDVRSGKCLKTLKGHSNYVFCCNFNPPSNLIISGS
ParentalFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVS
FDE.V.IW.VKTGKCLKTL.AHSDPVSAVHFN..GSLIVS.SYDGLCRIWD.ASGQCLKTL.DDDNPPVS
RetrocopyFDETVKIWEVKTGKCLKTLSAHSDPVSAVHFNCSGSLIVSGSYDGLCRIWDAASGQCLKTLVDDDNPPVS
ParentalFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
FVKFSPNGKYIL.ATLDNTLKLWDYS.G.CLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
RetrocopyFVKFSPNGKYILTATLDNTLKLWDYSRGRCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
ParentalQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSD
QTKEIVQKLQGHTDVVIS.ACHPTEN.IASAALENDKTIKLW.S.
RetrocopyQTKEIVQKLQGHTDVVISAACHPTENLIASAALENDKTIKLWMSN

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 2 .05 RPM 18 .61 RPM
bodymap2_adrenal 3 .50 RPM 23 .56 RPM
bodymap2_brain 1 .20 RPM 16 .71 RPM
bodymap2_breast 4 .46 RPM 21 .56 RPM
bodymap2_colon 1 .70 RPM 24 .36 RPM
bodymap2_heart 1 .85 RPM 15 .08 RPM
bodymap2_kidney 5 .01 RPM 26 .53 RPM
bodymap2_liver 1 .41 RPM 18 .42 RPM
bodymap2_lung 1 .95 RPM 11 .76 RPM
bodymap2_lymph_node 3 .53 RPM 26 .64 RPM
bodymap2_ovary 10 .72 RPM 40 .33 RPM
bodymap2_prostate 3 .46 RPM 23 .17 RPM
bodymap2_skeletal_muscle 1 .36 RPM 53 .02 RPM
bodymap2_testis 5 .94 RPM 82 .29 RPM
bodymap2_thyroid 9 .15 RPM 33 .90 RPM
bodymap2_white_blood_cells 6 .24 RPM 26 .54 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_11 in 53 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 3:122134727..122135393
ENCFF002CFW POLR2A 3:122134724..122135446
ENCFF002CFX POLR2A 3:122134736..122135449
ENCFF002CGN POLR2A 3:122134709..122135407
ENCFF002CHO POLR2A 3:122134582..122135550
ENCFF002CIH POLR2A 3:122134942..122135410
ENCFF002CIO POLR2A 3:122134676..122135440
ENCFF002CJE POLR2A 3:122134877..122135464
ENCFF002CJZ POLR2A 3:122134691..122135516
ENCFF002CKX POLR2A 3:122134710..122135424
ENCFF002CLM POLR2A 3:122134848..122135388
ENCFF002CMI POLR2A 3:122134672..122135516
ENCFF002COJ POLR2A 3:122134811..122135247
ENCFF002COJ POLR2A 3:122135028..122135464
ENCFF002CPG POLR2A 3:122134946..122135378
ENCFF002CPH POLR2A 3:122134919..122135309
ENCFF002CQA POLR2A 3:122134908..122135427
ENCFF002CQC POLR2A 3:122134736..122135426
ENCFF002CQE POLR2A 3:122134977..122135427
ENCFF002CQG POLR2A 3:122134973..122135416
ENCFF002CQI POLR2A 3:122134946..122135403
ENCFF002CQK POLR2A 3:122134692..122135433
ENCFF002CQM POLR2A 3:122134921..122135417
ENCFF002CQO POLR2A 3:122134681..122135454
ENCFF002CRK POLR2A 3:122134884..122135408
ENCFF002CRK POLR2A 3:122135084..122135608
ENCFF002CRO POLR2A 3:122135082..122135220
ENCFF002CSY POLR2A 3:122134646..122135528
ENCFF002CUP POLR2A 3:122135061..122135140
ENCFF002CUQ POLR2A 3:122134736..122135353
ENCFF002CVF POLR2A 3:122135028..122135219
ENCFF002CVJ POLR2A 3:122134791..122135339
ENCFF002CXM POLR2A 3:122134995..122135245
ENCFF002CXN POLR2A 3:122135017..122135273
ENCFF002CXO POLR2A 3:122135009..122135255
ENCFF002CXP POLR2A 3:122134922..122135326
ENCFF002CXQ POLR2A 3:122135062..122135712
ENCFF002CXR POLR2A 3:122134985..122135266
ENCFF002CZC POLR2A 3:122134653..122135584
ENCFF002CZD POLR2A 3:122134684..122135465
ENCFF002CZQ POLR2A 3:122134760..122135283
ENCFF002CZW POLR2A 3:122134549..122135499
ENCFF002CZY POLR2A 3:122134690..122135462
ENCFF002DAE POLR2A 3:122134972..122135282
ENCFF002DAE POLR2A 3:122134743..122135053
ENCFF002DAH POLR2A 3:122134984..122135268
ENCFF002DAK POLR2A 3:122135028..122135177
ENCFF002DAS POLR2A 3:122134874..122135350
ENCFF002DAV POLR2A 3:122134990..122135276
ENCFF002DAY POLR2A 3:122134997..122135321
ENCFF002DBB POLR2A 3:122135055..122135255
ENCFF002DBB POLR2A 3:122134787..122134987
ENCFF002DBE POLR2A 3:122134736..122135035
ENCFF002DBE POLR2A 3:122134924..122135206
ENCFF002DBO POLR2A 3:122134785..122135169
ENCFF002DBP POLR2A 3:122134824..122135016
ENCFF002DBP POLR2A 3:122134966..122135156
ENCFF002DBP POLR2A 3:122135222..122135386
ENCFF002DBQ POLR2A 3:122135011..122135267
ENCFF002DBT POLR2A 3:122135102..122135194

EST - click to see more details

4 EST(s) were mapped to retro_hsap_11 retrocopy
EST ID Start End Identity Match Mis-match Score
AV657168 122133548 122133931 99.7 328 1 326
AW627765 122133329 122133760 99.8 429 1 428
BQ372613 122133685 122134053 99.5 365 2 362
R83779 122133386 122133794 95.5 394 1 382

TSS - click to see more details

No TSS is located nearby retro_hsap_11 retrocopy 5' end.

Lab - click to see more details

retro_hsap_11 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_11 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_18
Gorilla gorilla retro_ggor_171
Macaca mulatta retro_mmul_190
Callithrix jacchus retro_cjac_1
Mus musculus retro_mmus_132
Rattus norvegicus retro_rnor_258
Bos taurus retro_btau_299
Sus scrofa retro_sscr_1
Canis familiaris retro_cfam_128
Equus caballus retro_ecab_82
Parental genes homology:
Parental genes homology involve 27 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111791 retrocopy
retro_amel_29,
Bos taurus ENSBTAG000000470311 retrocopy
retro_btau_299,
Canis familiaris ENSCAFG000000198301 retrocopy
retro_cfam_128,
Callithrix jacchus ENSCJAG000000101231 retrocopy
retro_cjac_1,
Cavia porcellus ENSCPOG000000147901 retrocopy
retro_cpor_12,
Dipodomys ordii ENSDORG000000150101 retrocopy
retro_dord_7,
Equus caballus ENSECAG000000173891 retrocopy
retro_ecab_82,
Echinops telfairi ENSETEG000000157311 retrocopy
retro_etel_15,
Felis catus ENSFCAG000000057121 retrocopy
retro_fcat_119,
Homo sapiens ENSG000000071682 retrocopies
retro_hsap_2144, retro_hsap_2292,
Homo sapiens ENSG000001226921 retrocopy
retro_hsap_457,
Homo sapiens ENSG00000196363 1 retrocopy
retro_hsap_11 ,
Gorilla gorilla ENSGGOG000000049972 retrocopies
retro_ggor_171, retro_ggor_2023,
Loxodonta africana ENSLAFG000000111921 retrocopy
retro_lafr_55,
Microcebus murinus ENSMICG000000080851 retrocopy
retro_mmur_34,
Myotis lucifugus ENSMLUG000000022361 retrocopy
retro_mluc_11,
Macaca mulatta ENSMMUG000000141591 retrocopy
retro_mmul_190,
Mustela putorius furoENSMPUG000000121841 retrocopy
retro_mputfur_2,
Mus musculus ENSMUSG000000269171 retrocopy
retro_mmus_132,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000236532 retrocopies
retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus ENSPVAG000000016661 retrocopy
retro_pvam_112,
Rattus norvegicus ENSRNOG000000082121 retrocopy
retro_rnor_258,
Sus scrofa ENSSSCG000000249121 retrocopy
retro_sscr_1,
Ictidomys tridecemlineatus ENSSTOG000000158991 retrocopy
retro_itri_117,
Drosophila melanogaster FBgn00400661 retrocopy
retro_dmel_69,

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 = 5 RPM Legend:


Library Retrogene expression
CEU_NA11831 3 .08 RPM
CEU_NA11843 2 .50 RPM
CEU_NA11930 3 .26 RPM
CEU_NA12004 1 .56 RPM
CEU_NA12400 3 .58 RPM
CEU_NA12751 4 .44 RPM
CEU_NA12760 3 .50 RPM
CEU_NA12827 2 .55 RPM
CEU_NA12872 3 .92 RPM
CEU_NA12873 3 .45 RPM
FIN_HG00183 4 .34 RPM
FIN_HG00277 3 .11 RPM
FIN_HG00315 3 .64 RPM
FIN_HG00321 3 .14 RPM
FIN_HG00328 4 .07 RPM
FIN_HG00338 2 .32 RPM
FIN_HG00349 2 .50 RPM
FIN_HG00375 3 .13 RPM
FIN_HG00377 1 .99 RPM
FIN_HG00378 3 .10 RPM
GBR_HG00099 2 .76 RPM
GBR_HG00111 3 .55 RPM
GBR_HG00114 2 .45 RPM
GBR_HG00119 4 .69 RPM
GBR_HG00131 4 .34 RPM
GBR_HG00133 4 .17 RPM
GBR_HG00134 3 .45 RPM
GBR_HG00137 3 .24 RPM
GBR_HG00142 5 .00 RPM
GBR_HG00143 3 .13 RPM
TSI_NA20512 2 .52 RPM
TSI_NA20513 4 .45 RPM
TSI_NA20518 2 .41 RPM
TSI_NA20532 2 .21 RPM
TSI_NA20538 3 .18 RPM
TSI_NA20756 2 .15 RPM
TSI_NA20765 3 .38 RPM
TSI_NA20771 2 .95 RPM
TSI_NA20786 2 .22 RPM
TSI_NA20798 3 .15 RPM
YRI_NA18870 3 .45 RPM
YRI_NA18907 2 .81 RPM
YRI_NA18916 4 .06 RPM
YRI_NA19093 2 .37 RPM
YRI_NA19099 3 .70 RPM
YRI_NA19114 2 .83 RPM
YRI_NA19118 2 .51 RPM
YRI_NA19213 2 .85 RPM
YRI_NA19214 3 .05 RPM
YRI_NA19223 4 .06 RPM

Indel association:

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





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