VPS39

General Information

Gene Name       : VPS39
Gene ID             : ENSG00000166887.15
Essential Gene : Yes

Functions

Localization

Domains (AlphaFold: VPS39)


Antibody Validation

Expression Level in Cell lines

Cell Line Gene Name Ensembl ID Rep1 TPM Rep2 TPM Average TPM Experiment ID
Gm12878VPS39ENSG00000166887.1530.4232.4031.41ENCSR000AEF
HepG2VPS39ENSG00000166887.1514.7217.1315.93ENCSR985KAT
K562VPS39ENSG00000166887.1520.0919.3119.70ENCSR000AEO

Assays

0 Released experiments are available on ENCORE database.







  eCLIP  

No eCLIP experiment available



  Antibody Validation  

No Antibody Primary Validation image or Secondary image available



  KD RNA-Seq  

No KD RNA-Seq experiment available



  RNA Bind-n-Seqn  

No RBNS experiment available



  Localization Image in HepG2  

No Localization Information available













RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela








RNA Targets

  • eCLIP assay for VPS39 is not avaliable on ENCORE database.



Proteins bound to RNA
  • VPS39 RNA is bound by 20 proteins.  







eCLIP assay for VPS39 is not avaliable on ENCORE database.





20 proteins are bound to VPS39 RNA:

Chr Start End Strand Matched Area log2(fold change) -log(p-value) Cell Line Binding Protein Name
chr154245294642453028-3'-UTR,CDS,intron-Distal,intron-Proximal3.474134.74886HepG2BCLAF1
chr154245283442452886-3'-UTR,intron-Distal,intron-Proximal5.9778831.70794K562LIN28B
chr154245220342452254-3'-UTR,intron-Distal3.977286.89197K562PUM2
chr154245111842451158-3'-UTR,intron-Distal3.460415.05294K562UPF1
chr154245227042452315-3'-UTR,intron-Distal4.045375.81489K562UPF1
chr154245102042451136-3'-UTR,intron-Distal4.178533.31904K562IGF2BP1
chr154245288642452934-3'-UTR,intron-Distal,intron-Proximal5.5521826.33504K562LIN28B
chr154245280442452930-3'-UTR,intron-Distal,intron-Proximal6.0979514.47018HepG2LIN28B
chr154245141442451442-3'-UTR,intron-Distal4.252893.54010K562UPF1
chr154245128742451325-3'-UTR,intron-Distal3.360403.66308K562UPF1
chr154245148342451571-3'-UTR,intron-Distal4.078938.24727K562UPF1
chr154245234842452398-3'-UTR,intron-Distal3.252895.45410K562UPF1
chr154245213842452274-3'-UTR,intron-Distal4.4506910.80623HepG2UPF1
chr154245120642451245-3'-UTR,intron-Distal4.706345.24231K562UPF1
chr154245215742452269-3'-UTR,intron-Distal3.322495.23218HepG2AKAP1
chr154245217342452246-3'-UTR,intron-Distal3.463498.16191K562UPF1
chr154245141142451550-3'-UTR,intron-Distal3.565994.81659HepG2UPF1
chr154250036542500485-5'-UTR,intron-Distal,intron-Proximal3.183115.42487HepG2NCBP2
chr154245791642457982-CDS,intron-Distal,intron-Proximal3.439933.86355HepG2PPIG
chr154247688942476899-CDS,intron-Distal,intron-Proximal4.450114.34038HepG2BCLAF1
chr154245833642458399-CDS,intron-Distal,intron-Proximal4.466164.08604HepG2PPIG
chr154245663642456696-CDS,intron-Distal,intron-Proximal3.069825.19836HepG2U2AF2
chr154245902142459107-CDS,intron-Distal,intron-Proximal4.057414.23295HepG2GRWD1
chr154248334642483398-CDS,intron-Distal,intron-Proximal3.662635.34337K562AQR
chr154245668042456740-CDS,intron-Distal,intron-Proximal4.281984.57682HepG2SF3B4
chr154247951342479561-CDS,intron-Distal3.815254.14015K562DDX24
chr154245896942459005-CDS,intron-Distal,intron-Proximal3.202103.07653K562ZNF622
chr154247666942476735-CDS,intron-Distal,intron-Proximal3.940996.23016HepG2PRPF8
chr154248331642483370-CDS,intron-Distal,intron-Proximal4.410255.24155K562BUD13
chr154247689242476950-CDS,intron-Distal,intron-Proximal4.683225.80027HepG2SF3B4
chr154245650742456595-CDS,intron-Distal,intron-Proximal4.540767.13970HepG2PRPF8
chr154247947242479513-CDS,intron-Distal3.623684.13746HepG2PPIG
chr154248368242483740-CDS,intron-Distal,intron-Proximal4.453163.79199HepG2PPIG
chr154247946842479498-CDS,intron-Distal,intron-Proximal5.344367.95223HepG2BCLAF1
chr154247672042476815-CDS,intron-Distal3.401643.75245K562BUD13
chr154247671942476801-CDS,intron-Distal3.156364.59873K562UCHL5
chr154249207042492160-CDS,intron-Distal,intron-Proximal3.961863.39325K562SRSF1
chr154248352842483603-intron-Distal,intron-Proximal3.662937.74495HepG2U2AF2
chr154247663842476686-intron-Distal,intron-Proximal3.694933.82719HepG2RBM22
chr154248361442483692-intron-Distal,intron-Proximal5.082406.04760K562AQR
chr154247114742471213-intron-Distal3.837973.64484HepG2HNRNPC
chr154248352542483590-intron-Distal4.422483.49003K562PRPF8
chr154247663542476695-intron-Distal,intron-Proximal4.384433.85435K562PRPF8
ChrStartEndStrandMatched Arealog2(fold change)-log(p-value)Cell LineBinding Protein Name




eCLIP assay for VPS39 is not avaliable on ENCORE database.



Diffrential Expression

  • The Knockdown/knockout assay for VPS39 is not available on ENCORE database.

  • 49 RBPs can affect the levels of VPS39.  








The Knockdown/knockout RNA-Seq assay for VPS39 is not available on ENCORE database.





49 RBPs can affect the gene expression of VPS39 :

Gene NameGene IDKDMeanCNMeanlog2(fold change) *-log(pval) **-log(padj) **Cell LineAffected by RBPBound by RBP
VPS39ENSG00000166887.111772.681101238.918100.516804.385503.22030HepG2ABCF1
VPS39ENSG00000166887.111455.242601111.341200.388905.386904.34990HepG2AKAP8L
VPS39ENSG00000166887.111703.579201154.184200.561606.645305.76470HepG2BOP1
VPS39ENSG00000166887.111389.153001103.917100.331502.224601.52680HepG2CIRBP
VPS39ENSG00000166887.111351.53920938.586600.525902.869202.08990HepG2CNOT7
VPS39ENSG00000166887.111307.511701023.058400.353805.059503.97770HepG2DDX19B
VPS39ENSG00000166887.111457.81150989.407400.559106.399405.41630HepG2DDX21
VPS39ENSG00000166887.111491.894001058.338700.495208.112607.07060HepG2DKC1
VPS39ENSG00000166887.111648.426101195.276500.463602.810702.11650HepG2EIF4B
VPS39ENSG00000166887.111581.884001080.891900.549307.027305.70150HepG2EWSR1
VPS39ENSG00000166887.111518.239701149.018500.401902.847802.17310HepG2G3BP1
VPS39ENSG00000166887.111514.044901219.817200.311602.063601.30220HepG2G3BP2
VPS39ENSG00000166887.111554.228301201.185000.371602.495001.88410HepG2GPKOW
VPS39ENSG00000166887.111253.778601056.071200.247502.398601.48190HepG2HDGF
VPS39ENSG00000166887.111563.26830961.256200.701509.786508.68120HepG2HNRNPA1
VPS39ENSG00000166887.111745.107001163.461700.584806.666205.61680HepG2HNRNPK
VPS39ENSG00000166887.11699.509501062.14480-0.6026010.273809.16790HepG2HNRNPU
VPS39ENSG00000166887.111774.565901167.955800.603406.370905.38380HepG2IGF2BP2
VPS39ENSG00000166887.112268.109301545.446700.553404.411803.35490HepG2LARP4
VPS39ENSG00000166887.111632.728401239.059600.397902.977702.29850HepG2MAGOH
VPS39ENSG00000166887.111592.991101245.997600.354302.221101.65260HepG2MATR3
VPS39ENSG00000166887.111492.261201135.794300.393702.865602.13180HepG2PABPC4
VPS39ENSG00000166887.11897.178201177.27370-0.392004.800803.81330HepG2PRPF4
VPS39ENSG00000166887.111007.12360756.810300.412102.556801.77960HepG2PRPF8
VPS39ENSG00000166887.111523.388001231.869000.306303.739803.12490HepG2PTBP1
VPS39ENSG00000166887.111319.969801126.756000.228202.335901.75810HepG2PUS1
VPS39ENSG00000166887.111990.197401704.502200.223502.213601.73670HepG2RBM22
VPS39ENSG00000166887.111716.371801370.956100.324103.974603.34800HepG2NELFE
VPS39ENSG00000166887.111526.798601276.851800.257802.687302.07840HepG2RECQL
VPS39ENSG00000166887.111841.091201483.211400.311702.396901.75360HepG2RPLP0
VPS39ENSG00000166887.111101.16960752.969600.548305.869705.01390HepG2RPS19
VPS39ENSG00000166887.111114.43870755.615000.560505.150103.87700HepG2SERBP1
VPS39ENSG00000166887.111656.873401282.543500.369405.047504.28900HepG2SF3B4
VPS39ENSG00000166887.112430.344001925.169700.336105.818005.16580HepG2SRFBP1
VPS39ENSG00000166887.111898.334701338.694100.503809.823509.05580HepG2SRSF1
VPS39ENSG00000166887.11737.469901089.09590-0.562509.279008.37270HepG2SRSF9
VPS39ENSG00000166887.112141.274801671.498200.357205.956205.25830HepG2SSB
VPS39ENSG00000166887.111112.71220844.500100.397803.489302.44320HepG2SUPT6H
VPS39ENSG00000166887.111441.833301203.260400.260902.397501.86930HepG2TAF15
VPS39ENSG00000166887.111494.015201298.382400.202401.986301.37820HepG2UPF1
VPS39ENSG00000166887.111003.979701253.54140-0.320303.488202.82990HepG2UTP3
VPS39ENSG00000166887.112022.595801427.976000.5021012.7350011.77880HepG2ZNF622
VPS39ENSG00000166887.112238.116901883.767300.248601.805801.31160K562AQR
VPS39ENSG00000166887.111499.206701048.603600.515604.892503.71800K562BOP1
VPS39ENSG00000166887.111464.873201134.538400.368602.864501.99440K562FMR1
VPS39ENSG00000166887.111428.152901064.353300.424103.952303.00810K562GPKOW
VPS39ENSG00000166887.111296.507501831.84720-0.498706.125504.99430K562GRSF1
VPS39ENSG00000166887.111143.322901644.90960-0.524808.199606.66870K562HNRNPU
VPS39ENSG00000166887.111165.039901421.05010-0.286602.316001.47800K562MATR3
VPS39ENSG00000166887.11920.172801266.94420-0.461404.381903.14450K562PCBP2
VPS39ENSG00000166887.111523.074301212.226800.329203.122102.26780K562POLR2G
VPS39ENSG00000166887.11991.573601383.48750-0.480505.661404.74100K562PTBP1
VPS39ENSG00000166887.111348.476101669.81440-0.308401.923601.45540K562PUS1
VPS39ENSG00000166887.111864.362901601.105600.219502.140301.41560K562SF3A3
VPS39ENSG00000166887.111336.928901012.512200.400902.683801.72340K562SF3B1
VPS39ENSG00000166887.111655.573401356.300000.287602.422701.75350K562SRSF1
VPS39ENSG00000166887.112289.051401720.448400.411907.882506.74390K562UPF1
Gene NameGene IDKDMeanCNMeanlog2(fold change)-log(pval)-log(padj)Cell LineAffected by RBPBound by RBP

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".






The Knockdown/knockout RNA-Seq assay for VPS39 is not available on ENCORE database.





12 RBPs can affect the splicing of VPS39 :

Event TypeGene NameGene IDchrStrandExonStartExonEnd2ndExonStart2ndExonEndupstreamESupstreamEEdownstreamESdownstreamEEdPSIp-valueFDRis_includedCell LineAffected by RBPBound by RBP
SEVPS39ENSG00000166887.11chr15-4248426342484296424836934248375842492093424921590.244000.000000.00000includedK562SRSF1
SEVPS39ENSG00000166887.11chr15-4245691242457087424565554245668442457193424573110.128000.000230.00997includedK562AKAP8L
SEVPS39ENSG00000166887.11chr15-4245691242457087424565554245668442457193424573110.410000.000000.00000includedHepG2HNRNPK
SEVPS39ENSG00000166887.11chr15-424813114248140642479955424800544248332242483365-0.099000.000750.00961excludedK562AQR
SEVPS39ENSG00000166887.11chr15-4245691242457087424565554245668442457193424573110.250000.000020.00720includedHepG2UCHL5
SEVPS39ENSG00000166887.11chr15-4245691242457087424565554245668442457193424573110.145000.000040.00109includedK562PUS1
SEVPS39ENSG00000166887.11chr15-424569124245708742456555424566844245719342457311-0.113000.000000.00014excludedHepG2SRSF1
SEVPS39ENSG00000166887.11chr15-424569124245708742456555424566844245719342457311-0.108000.000050.00435excludedHepG2SF3B4
SEVPS39ENSG00000166887.11chr15-4245367142453788424526284245302742453879424539710.053000.003810.09137includedK562UTP18
SEVPS39ENSG00000166887.11chr15-424833224248336542481311424814064248369342483758-0.145000.002790.07263excludedK562UTP18
SEVPS39ENSG00000166887.11chr15-4245691242457087424565554245668442457193424573110.086000.001140.04167includedK562HNRNPU
SEVPS39ENSG00000166887.11chr15-4245691242457079424565554245668442457193424573110.069000.000820.02367includedK562AGGF1
A3SSVPS39ENSG00000166887.11chr15-4248332242483570424833224248336542483693424837580.491000.000030.00537longerHepG2HNRNPK
A3SSVPS39ENSG00000166887.11chr15-4245295142453097424529514245302742453879424539710.085000.000800.06676longerK562AKAP8L
A3SSVPS39ENSG00000166887.11chr15-4245295142453097424529514245302742453879424539710.133000.001660.05605longerK562U2AF2
A3SSVPS39ENSG00000166887.11chr15-4246192142462090424619214246206442465920424660500.206000.000000.00001longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245719342457427424571934245731142457915424580140.100000.014290.07174longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245422942454426424542294245436442454529424546990.078000.000000.00002longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245295142453097424529514245302742453879424539710.052000.002410.01520longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245655542456718424565554245668442457193424574270.069000.003100.01900longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4247946842479582424794684247956142479955424800980.092000.001600.01057longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245876042458880424587604245884742458969424591110.070000.000110.00093longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4247064742470809424706474247076842476714424768980.120000.000820.00583longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245791542458134424579154245801442458356424584300.177000.000000.00002longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245452942454770424545294245467942455547424555930.154000.000000.00000longerK562AQR
A3SSVPS39ENSG00000166887.11chr15-4245295142453097424529514245302742453879424539710.054000.002450.09671longerK562PUS1
A3SSVPS39ENSG00000166887.11chr15-4246192142462090424619214246206442465920424660500.108000.001590.05850longerHepG2U2AF1
A3SSVPS39ENSG00000166887.11chr15-4246192142462090424619214246206442465920424660500.163000.001440.06048longerK562U2AF1
MXEVPS39ENSG00000166887.11chr15-4248131142481406424833224248336542479955424800544248369342483758-0.283000.000690.020682includedHepG2HNRNPK

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".





The Knockdown/knockout RNA-Seq assay for VPS39 is not avaliable on ENCORE database.