RetrogeneDB ID:

retro_hsap_3531

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:147728024..147729179(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220494
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YAP1
Ensembl ID:ENSG00000137693
Aliases:YAP1, YAP, YAP2, YAP65, YKI
Description:Yes-associated protein 1 [Source:HGNC Symbol;Acc:16262]


Retrocopy-Parental alignment summary:






>retro_hsap_3531
ATGGATCCCGGGCAGCAGCAACTGCCTCAACCGGCCCCCCAGGGCCAAGGGCAGCCACCGGCGCAGCGCCCCCCAGGGGC
AGGGCCCGCGGTCCAGACCAGGGCACCCGGCGCCCACGGCGACCCAGGCGGCGCCACAGGCAACCCCCACCGGGCGTCAG
ATCCTGCACGCCCGCGGGGACTGGGAGAGGAACCTGGAGGCGCTCTTCAACGCCTTCATGAACCCCAAGATGGCCAACGT
GCACCAGACCATGCCCATGAGGCTCCGGAAGCTGCCCGACTCTTTCAAGCCGCCCGAGCCCAAGTCCAACTCCCAACGGG
TCAGTACTGAGGCAGGCACCGCAGGAGCCCTGACTCCACAGCACGTTCGAGCTCATTCCTCTCCAGCTTCTCTGCAGTTG
GGAGCTGTTTCTCCTGGGACACTGACCCCCACTGGAGTAGTTTCTGGCCCAGCAGCTACACCCACAGCTCAGCATTTTCA
ACAGTCTTCTTTTGAGATACCTGATGATGTACCTCTACCAGCAGCTCGGGAGATGGCGAAGACATCTTCTGGTCAGAGAT
ACTTCTTAAATCACATCGATCAGAAAACAACACAGCAGGACCCCCAGGAAGACCATGCTGTCTCAGATGAATGTTATAGC
CAATCCACCAGTGCAGCAGAATATGATGAACTCGGCCTCAGGTCGTCTTCCTGATGGATGGGAACAAGCCATGACTCAGG
ATGGATAAATTTACTGTATAAACCATAAGAACAAGACCGCCTCTTGGCTAGACCCAAGGCTTGACACTCGTTTTGCCAGG
AACCTGAGAATCAGAGTGCTCCAGTGAAACAGCCACCACCCCTGGTTCCCCAGAGCCCACAAGGAGGCGTCATGGTGGCA
GCAACTCCAACCAGCAGCGACAGATGCGACCACAGCAACTGCAGATGGAGGAGAGGCTGCAGCTGAAACAGCAATAACTG
CTTCAGCAGGAGTTAGCACTGCGTAGCCAGTTACCAACACTGGAGCAGGACGGTGGGACTCAAAATCCAGTGTCTTCTCC
CAGGATGTCTCAGGAATTGAGAACAAGGACAGCCAATAGCTCAGATCCTTTCCTTAACCGTGGCACCTATCACTCTCGAG
ATGAGAGTACAGACAGTGGACTAAGCATGGGCAGC

ORF - retro_hsap_3531 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.49 %
Parental protein coverage: 79.92 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMDPGQQPPPQPAPQGQGQPPSQ-PPQGQGPPSGPGQPAPAATQAAPQAPPAGHQIVHVRGDSETDLEALF
MDPGQQ..PQPAPQGQGQPP.Q..PQGQGP.S.PG.PAP.ATQAAPQA.P.G.QI.H.RGD.E..LEALF
RetrocopyMDPGQQQLPQPAPQGQGQPPAQ>APQGQGPRSRPGHPAPTATQAAPQATPTGRQILHARGDWERNLEALF
ParentalNAVMNPKTANVPQTVPMRLRKLPDSFFKPPEPKSHSRQASTDAGTAGALTPQHVRAHSSPASLQLGAVSP
NA.MNPK.ANV.QT.PMRLRKLPDSF.KPPEPKS.S...ST.AGTAGALTPQHVRAHSSPASLQLGAVSP
RetrocopyNAFMNPKMANVHQTMPMRLRKLPDSF-KPPEPKSNSQRVSTEAGTAGALTPQHVRAHSSPASLQLGAVSP
ParentalGTLTPTGVVSGPAATPTAQHLRQSSFEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQD-PRKAMLS
GTLTPTGVVSGPAATPTAQH..QSSFEIPDDVPLPA..EMAKTSSGQRYFLNHIDQ.TT.QD.PRK.MLS
RetrocopyGTLTPTGVVSGPAATPTAQHFQQSSFEIPDDVPLPAAREMAKTSSGQRYFLNHIDQKTTQQD>PRKTMLS
ParentalQMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRFAMNQRI-SQSA
QMNV.A...PPVQQNMMNSASG.LPDGWEQAMTQDG.IY.INHKNKT.SWLDPRLD.RFA.N.RI.....
RetrocopyQMNVIA--NPPVQQNMMNSASGRLPDGWEQAMTQDG*IYCINHKNKTASWLDPRLDTRFARNLRI<QSAP
ParentalPVKQPPPLAPQSPQGGVM-GGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQELALRSQLPTLEQDGGTQ
....PP.L.PQSPQGGVM.GGSNSNQQ.QMR.QQLQME.ERL.LKQQ.LL.QELALRSQLPTLEQDGGTQ
RetrocopyVKQPPP-LVPQSPQGGVM<GGSNSNQQRQMRPQQLQME-ERLQLKQQ*LLQQELALRSQLPTLEQDGGTQ
ParentalNPVSSPGMSQELRTMTTNSSDPFLNSGTYHSRDESTDSGLSMSS
NPVSSP.MSQELRT.T.NSSDPFLN.GTYHSRDESTDSGLSM.S
RetrocopyNPVSSPRMSQELRTRTANSSDPFLNRGTYHSRDESTDSGLSMGS

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 212 .04 RPM
bodymap2_adrenal 0 .06 RPM 197 .39 RPM
bodymap2_brain 0 .00 RPM 54 .73 RPM
bodymap2_breast 0 .02 RPM 414 .19 RPM
bodymap2_colon 0 .00 RPM 266 .33 RPM
bodymap2_heart 0 .00 RPM 100 .13 RPM
bodymap2_kidney 0 .00 RPM 160 .11 RPM
bodymap2_liver 0 .00 RPM 58 .28 RPM
bodymap2_lung 0 .00 RPM 269 .50 RPM
bodymap2_lymph_node 0 .00 RPM 142 .77 RPM
bodymap2_ovary 0 .00 RPM 343 .88 RPM
bodymap2_prostate 0 .00 RPM 354 .84 RPM
bodymap2_skeletal_muscle 0 .02 RPM 86 .96 RPM
bodymap2_testis 0 .02 RPM 217 .94 RPM
bodymap2_thyroid 0 .00 RPM 227 .71 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3531 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3531 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_160372278 libraries472 libraries585 libraries312 libraries182 libraries

The graphical summary, for retro_hsap_3531 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3531 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3531 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2399
Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000006271 retrocopy
retro_cjac_4112,
Homo sapiens ENSG00000137693 1 retrocopy
retro_hsap_3531 ,
Otolemur garnettii ENSOGAG000000028852 retrocopies
retro_ogar_1565, retro_ogar_3345,
Pan troglodytes ENSPTRG000000042111 retrocopy
retro_ptro_2399,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 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 .02 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 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 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).





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