RetrogeneDB ID:

retro_hsap_1926

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:22596400..22597168(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229248
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WBP2
Ensembl ID:ENSG00000132471
Aliases:WBP2, WBP-2
Description:WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]


Retrocopy-Parental alignment summary:






>retro_hsap_1926
ATGGTGCTCAACGAGAGTCACTCAGAGGGCAGCAGAGTGATCGCCAACAACACTGAGAGCATCCCAATGCCCTACGATCA
TGTGAAACTTACGTTCAGTGACATGAATAATGTGCCAGAGGCCTCCAAAGGGACCAAGAAAGGCACCATCTACCTTACCC
CTTTCATCTTTCTGTCCAGGGCGAAGGATGCCACGCAGTCCTTCGTAATGTCATTTTATCTCTTGAAGGCCTATGAGATC
AAGCAGCCTGTGTTTGACACAAACTGCATCAAGGGAACAGTGAACACCGAAGCAGGCGGTGGCTGGGAAGGCTCTGCTTC
CGGCAAGTCCGCCTTCACGGCAGGGGGCGCCACTGAATCTGGACAGCAGGTGCTCCAGGTGACATCTCAAGCGTCCAGGG
GTGAAGCCCTCAGTGGAGCCTACGGCCACTCTCACGTGCCTGGCAGGACATGTGTCTTTCCCCCGCCAGTCACTAGTGGA
ATGTATCCCTGCCCTCCTGGCTGCCCTTCTCCACCACCTTCCCCTGAGTTCTATCCAGGACCTCCCAAGATGGACAGGGC
CATGGGGTATGTGCAACCCCCGCCACTGCCCTGTCCTGGGCCCATGGAACCTCCGGTCAGCCCAGATGTTCCCTGCACTC
CTGCAGCCGAAGCCAGGGCCACAAAAGCAGCTGCCAGCACCTATTATAACCCAGGCAAACCACACCACGTCTCCATGCCC
ACGAAGCAGCCTCCGCCATCTTACCCGAGGGAAGATAAGAAGACCCAG

ORF - retro_hsap_1926 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.18 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALNKNHSEGGGVIVNNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSF
M.LN..HSEG..VI.NNTESI.M.YDHV.LTF.DM.NVPEA.KGTKKGT.YLTP...IFLS..KDA.QSF
RetrocopyMVLNESHSEGSRVIANNTESIPMPYDHVKLTFSDMNNVPEASKGTKKGTIYLTPF--IFLSRAKDATQSF
ParentalMMPFYLMKDCEIKQPVFGANYIKGTVKAEAGGGWEGSASYKLTFTAGGAIEFGQRMLQVASQASRGEVPS
.M.FYL.K..EIKQPVF..N.IKGTV..EAGGGWEGSAS.K..FTAGGA.E.GQ..LQV.SQASRGE..S
RetrocopyVMSFYLLKAYEIKQPVFDTNCIKGTVNTEAGGGWEGSASGKSAFTAGGATESGQQVLQVTSQASRGEALS
ParentalGAYGYSYMPSGAYVYPPPVANGMYPCPPGYPYPPPPPEFYPGPPMMDGAMGYVQPPPPPYPGPMEPPVSG
GAYG.S..P....V.PPPV..GMYPCPPG.P.PPP.PEFYPGPP.MD.AMGYVQPPP.P.PGPMEPPVS.
RetrocopyGAYGHSHVPGRTCVFPPPVTSGMYPCPPGCPSPPPSPEFYPGPPKMDRAMGYVQPPPLPCPGPMEPPVS-
ParentalPDVPSTPAAEAKAAEAAASAYYNPGNPHNVYMPTSQPPPPPYYPPEDKKTQ
PDVP.TPAAEA.A..AAAS.YYNPG.PH.V.MPT.QPPP...YP.EDKKTQ
RetrocopyPDVPCTPAAEARATKAAASTYYNPGKPHHVSMPTKQPPPS--YPREDKKTQ

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 121 .08 RPM
bodymap2_adrenal 0 .00 RPM 79 .73 RPM
bodymap2_brain 0 .00 RPM 244 .03 RPM
bodymap2_breast 0 .00 RPM 72 .32 RPM
bodymap2_colon 0 .00 RPM 95 .15 RPM
bodymap2_heart 0 .00 RPM 61 .83 RPM
bodymap2_kidney 0 .00 RPM 59 .46 RPM
bodymap2_liver 0 .00 RPM 62 .95 RPM
bodymap2_lung 0 .00 RPM 166 .17 RPM
bodymap2_lymph_node 0 .00 RPM 76 .73 RPM
bodymap2_ovary 0 .00 RPM 74 .04 RPM
bodymap2_prostate 0 .00 RPM 117 .93 RPM
bodymap2_skeletal_muscle 0 .00 RPM 171 .11 RPM
bodymap2_testis 0 .00 RPM 90 .68 RPM
bodymap2_thyroid 0 .00 RPM 108 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 111 .81 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1926 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1926 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1926 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1926 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1926 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_15
Gorilla gorilla retro_ggor_1404
Pongo abelii retro_pabe_75
Parental genes homology:
Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000049461 retrocopy
retro_cfam_1038,
Callithrix jacchus ENSCJAG000000376191 retrocopy
retro_cjac_575,
Felis catus ENSFCAG000000057601 retrocopy
retro_fcat_1454,
Homo sapiens ENSG00000132471 1 retrocopy
retro_hsap_1926 ,
Gorilla gorilla ENSGGOG000000092412 retrocopies
retro_ggor_1404, retro_ggor_698,
Macropus eugenii ENSMEUG000000000701 retrocopy
retro_meug_579,
Macaca mulatta ENSMMUG000000093812 retrocopies
retro_mmul_1062, retro_mmul_854,
Monodelphis domestica ENSMODG000000077253 retrocopies
retro_mdom_1410, retro_mdom_1847, retro_mdom_375,
Mustela putorius furoENSMPUG000000137751 retrocopy
retro_mputfur_645,
Nomascus leucogenys ENSNLEG000000016251 retrocopy
retro_nleu_1214,
Ochotona princeps ENSOPRG000000060452 retrocopies
retro_opri_301, retro_opri_851,
Pongo abelii ENSPPYG000000086403 retrocopies
retro_pabe_693, retro_pabe_75, retro_pabe_913,
Pan troglodytes ENSPTRG000000096601 retrocopy
retro_ptro_15,
Ictidomys tridecemlineatus ENSSTOG000000214212 retrocopies
retro_itri_1585, retro_itri_660,

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 = 0.03 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 .00 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 .00 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 .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 .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 .03 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 .02 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).



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