RetrogeneDB ID:

retro_hsap_1878

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:30092060..30093036(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000260389
Aliases:WBP11P1, HsT3017
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WBP11
Ensembl ID:ENSG00000084463
Aliases:WBP11, NPWBP, SIPP1, WBP-11
Description:WW domain binding protein 11 [Source:HGNC Symbol;Acc:16461]


Retrocopy-Parental alignment summary:






>retro_hsap_1878
AAATAGCTGTGTGAAACCTTTGAACATATTCTATGACTCTATGAAAAAGAGGATCCAGATATTTAGAAAGAATTGAGAAA
GCTAGAAATAGAGTATGAACAGAAGAGGACTCAACCAATATTTGAATGCTGTCGAGAATGCCCAGCACGTGGAAGTGGAG
AGTATTCCTTTACCAGATATGCCACATGCTTCTTCTAACATTTTGATCCAGGAAATTCCACTTCCTGGTGCCCAGCCACC
CTCCATCCTTAAGAAACCCTCAGCCTGTGGACCTCCAACTCAGGCAGTTTCTATCCTTCTCTTCTTGGGACGTGGTGTTC
CACATTTGCCTCCTGGCAGAAAACCTCTTGGCCCTCCCCCTGGTCCACCCCCTCCTCAAGTCGTGCAGATGTATGGCCGT
AAAGTGGGTGTTGCCCTAGATCTTCCCCCTCCTAGGTGAGATGAAGGCATGGTACATAGTCCTGAAATTGCCCAGCGAGG
TCATGATGATGATGTTTTTAGCACCAGTGAAGATGATGGCTATCCTGAGGACGTGGATCAAGATAAGCATGATGACAGTA
CTGATGACAGTGACACCGACGGATCAGATTGAGAAAGTGTGCGCCATGATGATGGTGGGAGAGACAACAATGAAAAAAAG
AAGTCAGGTCTGAGTGTACGGTTTGCAGATATGCCTGGAAAATCAAGGAAGAAAAAAACCATGAAGGAACTGACTCCTCT
TCAAGCCACGATGCTTCGTATGGCAGGTCAAGAAATCCCTGAGGAGGGACGGGAAGTAGAGGAATTTTCAGAGGACAATG
ATGAAGATGATTCTGATGACTCTAAAGCAGAAAAACAATCACAAAAACACAATCAAGAGGAACTGCATTCTGATGGCACA
TCCACTGCTTCTTCACAGCAGCAGGCTCCCCGGCAGTCTGTTCCTCCTTCTCAGGTACAAGCACCTCCCATGCTTCACCA
TTACGGCCTCCTAGGC

ORF - retro_hsap_1878 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.65 %
Parental protein coverage: 54.86 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKKLRETFERILRLYEKENPDIYKELRKLEVEYEQK-RAQLSQYFDAVKNAQHVEVESIPLPDMPHAPSNI
K.L.ETFE.IL.LYEKE.PDI.KELRK...E.E...R..L.QY..AV.NAQHVEVESIPLPDMPHA.SNI
RetrocopyK*LCETFEHIL*LYEKEDPDI*KELRK--LEIEYE>RRGLNQYLNAVENAQHVEVESIPLPDMPHASSNI
ParentalLIQDIPLPGAQPPSILKKTSAYGPPTRAVSILPLLGHGVPRLPPGRKPPGPPPGPPPPQVVQMYGRKVGF
LIQ.IPLPGAQPPSILKK.SA.GPPT.AVSIL..LG.GVP.LPPGRKP.GPPPGPPPPQVVQMYGRKVG.
RetrocopyLIQEIPLPGAQPPSILKKPSACGPPTQAVSILLFLGRGVPHLPPGRKPLGPPPGPPPPQVVQMYGRKVGV
ParentalALDLPPRRRDEDMLYSPELAQRGHDDDVSSTSEDDGYPEDMDQDKHDDSTDDSDTDKSDGESDGDEFVHR
ALDLPP.R.DE.M..SPE.AQRGHDDDV.STSEDDGYP.....D...D..DDS.TD.SD......E.V..
RetrocopyALDLPPPR*DEGMVHSPEIAQRGHDDDVFSTSEDDGYP----EDVDQDKHDDS-TDDSDTDGSD*ESVRH
ParentalDNGERDNNEEKKSGLSVRFADMPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVEEFSEDDDEDDS
D.G.RDNNE.KKSGLSVRFADMPGKSRKKK..MKELTPLQA.MLRMAGQEIPEEGREVEEFSED.DEDDS
RetrocopyDDGGRDNNEKKKSGLSVRFADMPGKSRKKK-TMKELTPLQATMLRMAGQEIPEEGREVEEFSEDNDEDDS
ParentalDDSEAEKQSQKQHKEESHSDGTSTASSQQQAPPQSVPPSQIQAPPFLRPPGMPG
DDS.AEKQSQK...EE.HSDGTSTASSQQQAP.QSVPPSQ.QAPP.L...G..G
RetrocopyDDSKAEKQSQKHNQEELHSDGTSTASSQQQAPRQSVPPSQVQAPPMLHHYGLLG

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 80 .66 RPM
bodymap2_adrenal 0 .00 RPM 87 .18 RPM
bodymap2_brain 0 .00 RPM 91 .25 RPM
bodymap2_breast 0 .00 RPM 59 .48 RPM
bodymap2_colon 0 .00 RPM 58 .47 RPM
bodymap2_heart 0 .00 RPM 62 .42 RPM
bodymap2_kidney 0 .00 RPM 62 .37 RPM
bodymap2_liver 0 .00 RPM 25 .39 RPM
bodymap2_lung 0 .00 RPM 68 .92 RPM
bodymap2_lymph_node 0 .00 RPM 59 .06 RPM
bodymap2_ovary 0 .00 RPM 82 .52 RPM
bodymap2_prostate 0 .00 RPM 70 .08 RPM
bodymap2_skeletal_muscle 0 .00 RPM 88 .50 RPM
bodymap2_testis 0 .47 RPM 144 .45 RPM
bodymap2_thyroid 0 .00 RPM 125 .91 RPM
bodymap2_white_blood_cells 0 .00 RPM 108 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1878 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1878 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1878 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1878 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1878 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1260
Gorilla gorilla retro_ggor_1375
Pongo abelii retro_pabe_1558
Macaca mulatta retro_mmul_1329
Parental genes homology:
Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147591 retrocopy
retro_btau_20,
Canis familiaris ENSCAFG000000129262 retrocopies
retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus ENSCJAG000000216111 retrocopy
retro_cjac_1737,
Homo sapiens ENSG00000084463 2 retrocopies
retro_hsap_1878 , retro_hsap_4719,
Gorilla gorilla ENSGGOG000000044483 retrocopies
retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii ENSMEUG000000139711 retrocopy
retro_meug_1952,
Myotis lucifugus ENSMLUG000000152161 retrocopy
retro_mluc_1074,
Macaca mulatta ENSMMUG000000192991 retrocopy
retro_mmul_1329,
Monodelphis domestica ENSMODG000000179491 retrocopy
retro_mdom_143,
Mustela putorius furoENSMPUG000000116191 retrocopy
retro_mputfur_280,
Mus musculus ENSMUSG000000302161 retrocopy
retro_mmus_2740,
Nomascus leucogenys ENSNLEG000000039261 retrocopy
retro_nleu_2651,
Oryctolagus cuniculus ENSOCUG000000171771 retrocopy
retro_ocun_974,
Otolemur garnettii ENSOGAG000000105181 retrocopy
retro_ogar_207,
Ochotona princeps ENSOPRG000000150083 retrocopies
retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii ENSPPYG000000043233 retrocopies
retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes ENSPTRG000000047243 retrocopies
retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus ENSRNOG000000055053 retrocopies
retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus ENSRNOG000000495931 retrocopy
retro_rnor_740,
Sorex araneus ENSSARG000000070851 retrocopy
retro_sara_753,
Sarcophilus harrisii ENSSHAG000000166491 retrocopy
retro_shar_81,
Tupaia belangeri ENSTBEG000000033941 retrocopy
retro_tbel_2213,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 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 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 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 .02 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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