SMAD4

General Information

Gene Name       : SMAD4
Gene ID             : ENSG00000141646.13
Essential Gene : No

Functions

Localization

Domains (AlphaFold: SMAD4)


Antibody Validation

Expression Level in Cell lines

Cell Line Gene Name Ensembl ID Rep1 TPM Rep2 TPM Average TPM Experiment ID
Gm12878SMAD4ENSG00000141646.1344.2531.0937.67ENCSR000AEF
HepG2SMAD4ENSG00000141646.1348.7252.4350.58ENCSR985KAT
K562SMAD4ENSG00000141646.1325.0126.4725.74ENCSR000AEO

Assays

2 Released experiments are available on ENCORE database.

Assay TypeExp_NameENCODE IDTarget labelBiosampleStatusLinked AntibodyControlsMethodNote
knockdown followed by RNA-seq SMAD4-BGKcLV17-K562ENCSR965MSXSMAD4K562ReleasedENCSR516TLX   CRISPRKD% = 68.9,79.5
knockdown followed by RNA-seq SMAD4-BGHcLV18-HepG2ENCSR700FWDSMAD4HepG2ReleasedENCSR670KAS   CRISPRKD% = 91.5,90.3






  eCLIP  

No eCLIP experiment available



  Antibody Validation  
  GeneName    Antibody_DCC_ID    Product_ID    Lot_ID    Phosphate    HepG2 Primary Validation    K562 Primary Validation    HepG2 Secondary Validation    K562 Secondary Validation  
SMAD4ENCAB628ZTV7016822023880Released, ENCODE4BGHcLV18-45, Released, ENCODE4BGKcLV17-47, Released, ENCODE4


  KD RNA-Seq  
  GeneName    Cell_Line    Method    Exp_ID    Control_ID    Sample_reps    Control_reps    KD%    Status    Project    Note  
SMAD4K562CRISPRENCSR965MSXENCSR516TLXSMAD4-BGKcLV17-47,SMAD4-BGKcLV17-48NT-BGKcLV17-1,NT-BGKcLV17-268.9,79.5ReleasedENCODE4
SMAD4HepG2CRISPRENCSR700FWDENCSR670KASSMAD4-BGHcLV18-45,SMAD4-BGHcLV18-46NT-BGHcLV18-1,NT-BGHcLV18-291.5,90.3ReleasedENCODE4


  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
SMAD4Product_ID: 701682
Lot_ID: 2023880
Source: Thermo Fisher
Target Name: SMAD4-human		 SMAD4-HEPG2-CRISPR-701682.png<br>Caption: Western blot following CRISPR against SMAD4 in HepG2 whole cell lysate using SMAD4 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SMAD4. SMAD4 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 ThermoFisher_701682_2023880_SMAD4.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the SMAD4 specific antibody, 701682. Lane 1 is 2.5% of five million whole cell lysate input. Lanes 2 and 3 are 50% of IP enrichment from five million whole cell lysate using normal IgG antibody and the SMAD4-specific antibody, 701682. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
 SMAD4-K562-CRISPR-701682.png<br>Caption: Western blot following CRISPR against SMAD4 in K562 whole cell lysate using SMAD4 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SMAD4. SMAD4 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.








RNA Targets

  • eCLIP assay for SMAD4 is not avaliable on ENCORE database.



Proteins bound to RNA
  • SMAD4 RNA is bound by 24 proteins.  







eCLIP assay for SMAD4 is not avaliable on ENCORE database.





24 proteins are bound to SMAD4 RNA:

Chr Start End Strand Matched Area log2(fold change) -log(p-value) Cell Line Binding Protein Name
chr184858116148581373+3'-UTR,CDS,intron-Proximal3.027363.85159HepG2UCHL5
chr184860303648603090+3'-UTR,CDS3.494278.28018K562YBX3
chr184860585748605935+3'-UTR3.935064.13343HepG2FUBP3
chr184861088548610965+3'-UTR3.567424.40053K562GTF2F1
chr184860514648605204+3'-UTR3.707343.88742K562FAM120A
chr184858125648581263+3'-UTR,CDS3.722665.73361K562YBX3
chr184858126348581288+3'-UTR,CDS3.749559.26008K562YBX3
chr184861116848611244+3'-UTR4.377795.24781HepG2GRSF1
chr184858128848581329+3'-UTR,CDS3.531339.83933K562YBX3
chr184860485948604911+3'-UTR3.430563.28366HepG2BCLAF1
chr184860570848605749+3'-UTR3.248573.37207K562FAM120A
chr184860300948603036+3'-UTR,CDS3.664076.42513K562YBX3
chr184861087948610961+3'-UTR5.1322213.97136K562FAM120A
chr184858109448581192+3'-UTR,CDS,intron-Proximal5.369656.40247K562SF3B4
chr184860308448603176+3'-UTR,CDS,intron-Proximal3.619066.29405HepG2PRPF8
chr184855692948556987+5'-UTR,intron-Distal5.448845.58036HepG2EFTUD2
chr184855681948556946+5'-UTR,intron-Distal3.5166220.03640HepG2DDX3X
chr184855670148556789+5'-UTR,intron-Distal,intron-Proximal3.168636.63304K562DROSHA
chr184855675848556800+5'-UTR,intron-Distal4.251356.08301HepG2EFTUD2
chr184855687048556903+5'-UTR,intron-Distal3.500724.12229HepG2EFTUD2
chr184855669448556819+5'-UTR,intron-Distal,intron-Proximal3.1295019.54534HepG2DDX3X
chr184857360248573672+3'-UTR,CDS,intron-Distal,intron-Proximal3.310873.17151K562UCHL5
chr184857514648575257+3'-UTR,CDS,intron-Proximal3.261626.80151HepG2BCLAF1
chr184857358948573669+3'-UTR,CDS,intron-Distal,intron-Proximal3.438447.74581HepG2BCLAF1
chr184857566148575730+3'-UTR,CDS,intron-Proximal5.175075.05356HepG2PRPF8
chr184859179948591864+CDS,intron-Distal3.328256.01266K562LIN28B
chr184857522848575271+3'-UTR,CDS,intron-Proximal4.734823.62536K562AQR
chr184857562648575711+3'-UTR,CDS,intron-Proximal4.535847.50107K562AQR
chr184859339848593557+CDS,intron-Distal3.026886.91034HepG2BCLAF1
chr184859187548591969+CDS,intron-Distal3.195665.80244K562LIN28B
chr184857564948575709+3'-UTR,CDS,intron-Proximal5.103137.46464K562PRPF8
chr184857346548573526+3'-UTR,CDS,intron-Distal3.922595.06180HepG2BCLAF1
chr184857342048573465+3'-UTR,CDS,intron-Distal3.583553.57857HepG2BCLAF1
chr184859176648591866+CDS,intron-Distal,intron-Proximal3.105617.66226HepG2U2AF2
chr184856741548567474+intron-Distal4.434554.58231HepG2HNRNPK
chr184858101848581107+intron-Distal,intron-Proximal3.381264.74253K562KHSRP
chr184856154448561631+intron-Distal4.7933110.89104HepG2PTBP1
chr184855699948557063+intron-Distal,intron-Proximal4.149204.66211HepG2XRN2
chr184855739448557469+intron-Distal3.100163.05068HepG2U2AF2
chr184858507348585156+intron-Distal4.170304.54401K562KHSRP
chr184859200048592094+intron-Distal,intron-Proximal3.749744.70224K562KHSRP
chr184856149748561544+intron-Distal3.700366.41195HepG2PTBP1
chr184855700448557060+intron-Distal,intron-Proximal4.468188.44359HepG2EFTUD2
chr184857546348575611+intron-Distal,intron-Proximal3.522895.57010K562KHSRP
chr184858631748586410+intron-Distal,intron-Proximal3.559684.35635K562PRPF8
chr184856151248561586+intron-Distal3.950824.57279K562PTBP1
chr184856550748565608+intron-Distal3.544635.35459K562KHSRP
chr184855957348559620+intron-Distal3.905443.84404HepG2HNRNPC
chr184857050648570557+intron-Distal4.332853.35169HepG2U2AF2
chr184858634248586423+intron-Distal,intron-Proximal4.280525.32062K562EFTUD2
chr184855707448557151+intron-Distal,intron-Proximal3.577155.19517HepG2EFTUD2
chr184858769048587745+intron-Distal4.452554.85866HepG2QKI
chr184859167648591745+intron-Distal,intron-Proximal4.701349.01206HepG2U2AF2
chr184856686548567007+intron-Distal3.635234.64467HepG2HNRNPL
chr184857225548572347+intron-Distal4.316624.31512K562KHSRP
chr184857779048577932+intron-Distal,intron-Proximal4.499056.28383K562KHSRP
chr184856869648568778+intron-Distal5.835839.42242HepG2PCBP2
chr184857571248575784+intron-Proximal3.031364.31458HepG2TIAL1
ChrStartEndStrandMatched Arealog2(fold change)-log(p-value)Cell LineBinding Protein Name




eCLIP assay for SMAD4 is not avaliable on ENCORE database.



Diffrential Expression

  • The Knockdown/knockout assay for SMAD4 is not available on ENCORE database.

  • 79 RBPs can affect the levels of SMAD4.  








The Knockdown/knockout RNA-Seq assay for SMAD4 is not available on ENCORE database.





79 RBPs can affect the gene expression of SMAD4 :

Gene NameGene IDKDMeanCNMeanlog2(fold change) *-log(pval) **-log(padj) **Cell LineAffected by RBPBound by RBP
SMAD4ENSG00000141646.91205.250201388.63440-0.204302.010501.47710HepG2ACO1
SMAD4ENSG00000141646.91482.185102315.52270-0.643606.226805.46560HepG2AKAP1
SMAD4ENSG00000141646.9832.778901096.23940-0.396602.363901.49960HepG2BCCIP
SMAD4ENSG00000141646.91445.911201743.35070-0.269902.854702.20370HepG2CELF1
SMAD4ENSG00000141646.91663.031101874.51550-0.172701.968101.32670HepG2DAZAP1
SMAD4ENSG00000141646.91097.104401284.30090-0.227302.419301.63350HepG2DDX19B
SMAD4ENSG00000141646.91373.387102218.07640-0.691608.141707.11970HepG2DDX3X
SMAD4ENSG00000141646.9802.812301077.84010-0.425002.665701.90370HepG2DDX55
SMAD4ENSG00000141646.91502.760401905.41870-0.342502.172701.61900HepG2DDX6
SMAD4ENSG00000141646.9784.931301068.70500-0.445205.266804.32430HepG2DNAJC21
SMAD4ENSG00000141646.9733.962601059.24750-0.529309.184108.07740HepG2DNAJC2
SMAD4ENSG00000141646.91372.586301831.68040-0.416303.311202.66660HepG2EIF2S1
SMAD4ENSG00000141646.91594.165702024.20040-0.344602.144201.57870HepG2EIF4A3
SMAD4ENSG00000141646.91539.112101970.88460-0.356701.890801.31490HepG2EIF4B
SMAD4ENSG00000141646.92615.562502281.343300.197102.171401.62660HepG2ETF1
SMAD4ENSG00000141646.91482.636402042.39900-0.462104.107203.27550HepG2FXR1
SMAD4ENSG00000141646.91396.616101894.59000-0.440003.423802.68760HepG2G3BP1
SMAD4ENSG00000141646.91414.826701918.52470-0.439404.162903.32070HepG2HNRNPK
SMAD4ENSG00000141646.91401.458401707.53580-0.285004.187503.37100HepG2HNRNPL
SMAD4ENSG00000141646.9732.079201192.18420-0.7035014.2419012.95520HepG2HNRNPU
SMAD4ENSG00000141646.91379.304401925.79710-0.481504.413303.57620HepG2IGF2BP2
SMAD4ENSG00000141646.91116.143301807.32700-0.695302.925201.91440HepG2IGF2BP3
SMAD4ENSG00000141646.91042.733801217.77780-0.223902.349901.66650HepG2ILF2
SMAD4ENSG00000141646.91474.362802043.11240-0.470704.121103.32310HepG2MAGOH
SMAD4ENSG00000141646.91420.698602054.53670-0.532204.589703.79490HepG2MATR3
SMAD4ENSG00000141646.91304.091702102.92390-0.689407.788706.75160HepG2NCBP2
SMAD4ENSG00000141646.91540.665801858.76650-0.270802.613901.87300HepG2NOL12
SMAD4ENSG00000141646.9692.07710989.78310-0.516202.282901.30200HepG2NONO
SMAD4ENSG00000141646.91438.885801872.75100-0.380202.807502.08100HepG2PABPC4
SMAD4ENSG00000141646.9889.332001180.06670-0.408105.200604.08600HepG2PARN
SMAD4ENSG00000141646.91272.406301746.12300-0.456607.792506.85640HepG2PCBP1
SMAD4ENSG00000141646.91365.627301776.78960-0.379705.418004.70680HepG2PTBP1
SMAD4ENSG00000141646.91327.194201774.35930-0.418904.325303.59960HepG2PUF60
SMAD4ENSG00000141646.91491.030001883.56530-0.337206.057605.24990HepG2PUM1
SMAD4ENSG00000141646.91411.991001882.18660-0.414705.062504.16940HepG2PUM2
SMAD4ENSG00000141646.91108.995901414.41840-0.351004.950204.16970HepG2PUS1
SMAD4ENSG00000141646.92109.042901746.382500.272102.372301.74270HepG2RBM25
SMAD4ENSG00000141646.91588.727201977.35960-0.315704.084903.45060HepG2NELFE
SMAD4ENSG00000141646.9514.85630774.19890-0.588505.586104.74700HepG2RPS19
SMAD4ENSG00000141646.91299.490801680.67800-0.371102.036101.35010HepG2RPS3A
SMAD4ENSG00000141646.9696.681101061.69670-0.6078010.770009.62840HepG2SAFB2
SMAD4ENSG00000141646.91516.191801849.78820-0.286903.435102.78500HepG2SF3B4
SMAD4ENSG00000141646.9872.487101238.12460-0.505009.516008.43680HepG2SMN1
SMAD4ENSG00000141646.91570.783401930.81070-0.297704.049603.50460HepG2SRSF1
SMAD4ENSG00000141646.91463.153701111.047600.397102.393801.47020HepG2SRSF3
SMAD4ENSG00000141646.91423.276201751.92680-0.299703.759903.05160HepG2SRSF5
SMAD4ENSG00000141646.91368.158201992.41870-0.5423012.9667011.78580HepG2SUCLG1
SMAD4ENSG00000141646.9507.95080719.15900-0.501602.807201.80510HepG2TFIP11
SMAD4ENSG00000141646.9886.557301158.45520-0.385903.771203.20680HepG2TIAL1
SMAD4ENSG00000141646.9665.296301168.78360-0.8129018.1270016.84890HepG2TRIM56
SMAD4ENSG00000141646.91390.748201733.48130-0.317802.845001.95930HepG2TUFM
SMAD4ENSG00000141646.9907.254701194.37530-0.396702.929002.28360HepG2U2AF1
SMAD4ENSG00000141646.91446.756601834.86760-0.342902.222401.47660HepG2UBE2L3
SMAD4ENSG00000141646.91011.803201338.09210-0.403205.942804.98100HepG2UPF1
SMAD4ENSG00000141646.9975.939601291.87390-0.404605.477904.68280HepG2UTP3
SMAD4ENSG00000141646.91013.415501403.33120-0.469602.775801.71890HepG2XRCC6
SMAD4ENSG00000141646.9818.618401056.21150-0.367602.358601.68460HepG2XRN2
SMAD4ENSG00000141646.91280.352501471.64390-0.200902.216001.71130HepG2ZNF622
SMAD4ENSG00000141646.91627.325701367.960000.250402.840402.26550K562AGGF1
SMAD4ENSG00000141646.92249.729201697.684500.406103.982403.30300K562AQR
SMAD4ENSG00000141646.91807.456101304.262400.470602.259401.31880K562CNOT7
SMAD4ENSG00000141646.92919.618402423.359100.268702.594201.65010K562CELF1
SMAD4ENSG00000141646.91280.333001557.22330-0.282503.372602.66350K562DDX47
SMAD4ENSG00000141646.9887.767801130.09470-0.348203.581902.78060K562EIF2S2
SMAD4ENSG00000141646.91308.15690987.594500.405402.786301.74540K562EIF3D
SMAD4ENSG00000141646.9791.47610965.22310-0.286302.010101.32250K562EIF3G
SMAD4ENSG00000141646.91312.608901039.158200.336903.470002.19400K562GLRX3
SMAD4ENSG00000141646.91490.024901171.497900.346903.227402.06550K562HNRNPA1
SMAD4ENSG00000141646.91885.976501510.584100.320102.686501.87480K562KIF1C
SMAD4ENSG00000141646.91581.098601253.704300.334602.791001.80710K562PCBP2
SMAD4ENSG00000141646.91534.142101129.560300.441603.387202.46590K562PCBP3
SMAD4ENSG00000141646.91147.21350897.388700.354202.630101.89850K562PRPF8
SMAD4ENSG00000141646.91087.761601368.88160-0.331602.991602.30370K562PTBP1
SMAD4ENSG00000141646.92967.210602150.295900.464505.802304.62560K562PUF60
SMAD4ENSG00000141646.92020.408001411.583600.517205.441604.71190K562PUS1
SMAD4ENSG00000141646.91885.777701375.436100.455206.753805.85360K562RBM15
SMAD4ENSG00000141646.91047.554801381.45390-0.399203.202702.01720K562NELFE
SMAD4ENSG00000141646.91725.410301038.610700.732203.082601.75940K562SNRNP200
SMAD4ENSG00000141646.91432.996701227.158200.223602.370001.49520K562SRPK2
SMAD4ENSG00000141646.9902.291201341.92050-0.572607.268306.13140K562SRSF1
SMAD4ENSG00000141646.91076.687501310.11180-0.283102.265001.53160K562TIA1
SMAD4ENSG00000141646.91557.171201146.977200.441005.333804.22340K562U2AF2
SMAD4ENSG00000141646.91386.512901145.283700.275702.876102.01280K562WDR43
SMAD4ENSG00000141646.92554.947002012.021900.344503.609402.12420K562WRN
SMAD4ENSG00000141646.92548.571201912.213300.414304.615203.45850K562ZC3H8
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 SMAD4 is not available on ENCORE database.





4 RBPs can affect the splicing of SMAD4 :

Event TypeGene NameGene IDchrStrandExonStartExonEnd2ndExonStart2ndExonEndupstreamESupstreamEEdownstreamESdownstreamEEdPSIp-valueFDRis_includedCell LineAffected by RBPBound by RBP
SESMAD4ENSG00000141646.9chr18+4860367648603789486030074860314648604625486052400.294000.000210.00576includedK562SRSF1
SESMAD4ENSG00000141646.9chr18+485844944858461448581150485813634858623548586286-0.275000.000380.00913excludedHepG2U2AF1
SESMAD4ENSG00000141646.9chr18+4860367648603789486030074860314648604625486052400.082000.003180.06793includedHepG2HNRNPK
SESMAD4ENSG00000141646.9chr18+4860367648603789486030074860314648604625486052400.124000.000420.01253includedHepG2SRSF1
SESMAD4ENSG00000141646.9chr18+4860367648603789486030074860314648604625486052400.297000.001250.02320includedK562HNRNPC

*: "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 SMAD4 is not avaliable on ENCORE database.