CPSF3

General Information

Gene Name       : CPSF3
Gene ID             : ENSG00000119203.13
Essential Gene : Yes

Functions

Localization

Domains (AlphaFold: CPSF3)


Antibody Validation

 View validation images for all CPSF3 antibodies

Expression Level in Cell lines

Cell Line Gene Name Ensembl ID Rep1 TPM Rep2 TPM Average TPM Experiment ID
Gm12878CPSF3ENSG00000119203.1372.9556.8164.88ENCSR000AEF
HepG2CPSF3ENSG00000119203.1355.3471.7363.54ENCSR985KAT
K562CPSF3ENSG00000119203.1375.5563.5569.55ENCSR000AEO

Assays

2 Released experiments are available on ENCORE database.

Assay TypeExp_NameENCODE IDTarget labelBiosampleStatusLinked AntibodyControlsMethodNote
knockdown followed by RNA-seq CPSF3-BGKcLV28-K562ENCSR970WRVCPSF3K562ReleasedENCSR220DTX   CRISPRKD% = 69.0,72.8
knockdown followed by RNA-seq CPSF3-BGHcLV29-HepG2ENCSR958OFRCPSF3HepG2ReleasedENCSR462MFN   CRISPRKD% = 53.4,54.2






  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  
CPSF3ENCAB903JBSA301-090A1Released, ENCODE4BGHcLV29-35, Released, ENCODE4BGKcLV28-35, Released, ENCODE4
CPSF3ENCAB959SOTA301-091A1Released, ENCODE4BGHcLV29-35, Released, ENCODE4


  KD RNA-Seq  
  GeneName    Cell_Line    Method    Exp_ID    Control_ID    Sample_reps    Control_reps    KD%    Status    Project    Note  
CPSF3K562CRISPRENCSR970WRVENCSR220DTXCPSF3-BGKcLV28-35,CPSF3-BGKcLV28-36NT-BGKcLV28-1,NT-BGKcLV28-269.0,72.8ReleasedENCODE4
CPSF3HepG2CRISPRENCSR958OFRENCSR462MFNCPSF3-BGHcLV29-35,CPSF3-BGHcLV29-36NT-BGHcLV29-1,NT-BGHcLV29-253.4,54.2ReleasedENCODE4


  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
CPSF3Product_ID: A301-090A
Lot_ID: 1
Source: Bethyl Labs
Target Name: CPSF3-human		 CPSF3-HEPG2-CRISPR-A301-090A.png<br>Caption: Western blot following CRISPR against CPSF3 in HepG2 whole cell lysate using CPSF3 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CPSF3. CPSF3 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
 Bethyl_A301-090A_1_CPSF3.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the CPSF3 specific antibody, A301-090A. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the CPSF3-specific antibody, A301-090A. 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.
 CPSF3-K562-CRISPR-A301-090A.png<br>Caption: Western blot following CRISPR against CPSF3 in K562 whole cell lysate using CPSF3 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CPSF3. CPSF3 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
CPSF3Product_ID: A301-091A
Lot_ID: 1
Source: Bethyl Labs
Target Name: CPSF3-human		 Bethyl_A301-091A_1_CPSF3.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the CPSF3 specific antibody, A301-091A. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the CPSF3-specific antibody, A301-091A. 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.








RNA Targets

  • eCLIP assay for CPSF3 is not avaliable on ENCORE database.



Proteins bound to RNA
  • CPSF3 RNA is bound by 14 proteins.  







eCLIP assay for CPSF3 is not avaliable on ENCORE database.





14 proteins are bound to CPSF3 RNA:

Chr Start End Strand Matched Area log2(fold change) -log(p-value) Cell Line Binding Protein Name
chr296130449613158+3'-UTR,CDS,intron-Proximal3.105383.18660HepG2PABPN1
chr295819239581977+CDS,intron-Proximal3.786896.17334HepG2U2AF2
chr295740089574042+CDS4.776505.68196HepG2BCLAF1
chr295820569582105+CDS4.080349.39582HepG2BCLAF1
chr295764079576493+CDS,intron-Proximal4.8949016.73160K562LIN28B
chr295883769588464+CDS3.729545.08388K562UCHL5
chr295836449583669+CDS3.998595.79432HepG2BCLAF1
chr295763399576399+CDS,intron-Proximal3.434676.50801HepG2BCLAF1
chr295884009588469+CDS3.964127.65975HepG2BCLAF1
chr296115439611554+CDS3.512874.09885HepG2BCLAF1
chr295819639581981+CDS4.723045.23259HepG2BCLAF1
chr295764439576527+CDS,intron-Proximal4.165445.34978HepG2PRPF8
chr295806669580698+CDS3.828133.02250K562YBX3
chr295930539593093+CDS3.495385.15500HepG2BCLAF1
chr295971229597155+CDS3.054104.61799HepG2BCLAF1
chr295726059572678+CDS,intron-Proximal4.272783.63072HepG2AQR
chr295819819582004+CDS3.998595.79432HepG2BCLAF1
chr295763419576465+CDS3.006194.40043HepG2GRWD1
chr295726429572690+CDS4.138643.66349K562LIN28B
chr295708869570945+CDS3.141263.00343HepG2GRWD1
chr295764139576469+CDS3.264125.00751HepG2BCLAF1
chr296064669606543+intron-Distal3.782963.27276HepG2HNRNPL
chr295658799566065+intron-Distal4.820387.07589HepG2HNRNPL
chr295817639581826+intron-Distal4.719516.21813K562TIA1
chr296061139606206+intron-Distal3.661463.19036K562HNRNPL
chr296065629606659+intron-Distal4.026573.33101HepG2AGGF1
chr295817489581803+intron-Distal3.951883.61881HepG2TIAL1
chr295815239581567+intron-Distal3.740343.62357HepG2U2AF2
chr296060009606080+intron-Distal5.201667.88608K562AGGF1
chr296065319606637+intron-Distal4.9326512.18390K562AGGF1
chr295814149581475+intron-Distal4.170304.79477K562KHSRP
chr295816439581694+intron-Distal3.820193.67656K562U2AF2
chr295818049581870+intron-Distal,intron-Proximal4.110984.72162K562KHSRP
ChrStartEndStrandMatched Arealog2(fold change)-log(p-value)Cell LineBinding Protein Name




eCLIP assay for CPSF3 is not avaliable on ENCORE database.



Diffrential Expression

  • The Knockdown/knockout assay for CPSF3 is not available on ENCORE database.

  • 102 RBPs can affect the levels of CPSF3.  








The Knockdown/knockout RNA-Seq assay for CPSF3 is not available on ENCORE database.





102 RBPs can affect the gene expression of CPSF3 :

Gene NameGene IDKDMeanCNMeanlog2(fold change) *-log(pval) **-log(padj) **Cell LineAffected by RBPBound by RBP
CPSF3ENSG00000119203.91631.745701315.072300.311204.336503.60810HepG2ACO1
CPSF3ENSG00000119203.91596.875302130.65280-0.416007.299706.27120HepG2AUH
CPSF3ENSG00000119203.9735.487801171.06000-0.671006.038804.76800HepG2BCLAF1
CPSF3ENSG00000119203.9800.809001318.85540-0.719809.298008.28210HepG2BOP1
CPSF3ENSG00000119203.91014.213101314.89770-0.374605.644304.75560HepG2CKAP4
CPSF3ENSG00000119203.9650.999201210.77580-0.8952012.1872010.86170HepG2CPSF6
CPSF3ENSG00000119203.91753.985702225.77560-0.343706.226405.17750HepG2DAZAP1
CPSF3ENSG00000119203.9784.057201435.18500-0.872209.570108.49440HepG2DDX6
CPSF3ENSG00000119203.9806.361901261.46170-0.6456010.902109.58230HepG2DNAJC21
CPSF3ENSG00000119203.9970.736501250.40800-0.365205.390704.52570HepG2DNAJC2
CPSF3ENSG00000119203.9850.897901177.82580-0.469103.024101.85940HepG2AGO1
CPSF3ENSG00000119203.9755.473301379.83590-0.8690010.781609.65860HepG2EIF2S1
CPSF3ENSG00000119203.91153.747801524.95710-0.402402.576301.95870HepG2EIF4A3
CPSF3ENSG00000119203.91136.993801484.61420-0.384902.009101.41730HepG2EIF4B
CPSF3ENSG00000119203.91883.475002195.99760-0.221502.334801.55460HepG2EIF4G1
CPSF3ENSG00000119203.91310.598002103.60120-0.682609.239907.78820HepG2EIF4G2
CPSF3ENSG00000119203.91866.611402446.31050-0.390206.687305.81970HepG2ETF1
CPSF3ENSG00000119203.91048.763701372.49410-0.388102.591301.96890HepG2GPKOW
CPSF3ENSG00000119203.9940.660501255.58500-0.416605.864804.50220HepG2HDGF
CPSF3ENSG00000119203.9768.154401273.54780-0.729409.704808.60330HepG2HNRNPA1
CPSF3ENSG00000119203.91162.493601743.81150-0.5850011.6232010.29080HepG2HNRNPF
CPSF3ENSG00000119203.91770.222502027.46420-0.195702.290501.66870HepG2HNRNPL
CPSF3ENSG00000119203.9759.731601309.79780-0.785809.528308.44030HepG2HNRNPLL
CPSF3ENSG00000119203.91228.322701717.16530-0.483306.088305.05530HepG2IGF2BP1
CPSF3ENSG00000119203.91087.846501450.76170-0.415303.039302.33680HepG2IGF2BP2
CPSF3ENSG00000119203.91247.627401437.45130-0.204302.238701.57060HepG2ILF2
CPSF3ENSG00000119203.91025.049701202.21020-0.230002.412901.46010HepG2KIF1C
CPSF3ENSG00000119203.91684.430502255.00920-0.420902.793401.95900HepG2LARP4
CPSF3ENSG00000119203.91224.959101584.05830-0.370902.487401.88530HepG2NCBP2
CPSF3ENSG00000119203.91809.547102207.08280-0.286502.906102.12510HepG2NOL12
CPSF3ENSG00000119203.9574.49890984.24900-0.776704.780003.59010HepG2PABPC1
CPSF3ENSG00000119203.91038.964701410.84740-0.441403.337402.54870HepG2PABPC4
CPSF3ENSG00000119203.9785.359301386.43100-0.8200019.6006018.22170HepG2PCBP1
CPSF3ENSG00000119203.9953.804101255.14690-0.396104.635003.70570HepG2PPIL4
CPSF3ENSG00000119203.9740.541501022.24400-0.465103.220402.35540HepG2PRPF8
CPSF3ENSG00000119203.91437.540202106.89650-0.551507.266006.35850HepG2PUF60
CPSF3ENSG00000119203.91764.286102236.61380-0.342206.493805.66490HepG2PUM1
CPSF3ENSG00000119203.91154.079101339.50280-0.215001.985301.44450HepG2PUS1
CPSF3ENSG00000119203.9684.025301493.53880-1.126609.417908.17150HepG2RAVER1
CPSF3ENSG00000119203.91741.952802044.65540-0.231202.370601.88100HepG2RBM22
CPSF3ENSG00000119203.91860.940501570.023600.245102.637702.10690HepG2NELFE
CPSF3ENSG00000119203.91078.967701878.38100-0.7998012.5115011.24500HepG2RPLP0
CPSF3ENSG00000119203.91035.092901467.04900-0.503202.888301.92540HepG2RPS10
CPSF3ENSG00000119203.9784.01290960.27040-0.292601.962201.43680HepG2RPS19
CPSF3ENSG00000119203.9702.623101011.21940-0.525303.634202.75000HepG2RRP9
CPSF3ENSG00000119203.91046.771301253.19890-0.259702.804202.15670HepG2SAFB2
CPSF3ENSG00000119203.91418.047002020.28830-0.5107011.8382010.56040HepG2SLBP
CPSF3ENSG00000119203.92032.291302309.34980-0.184402.116801.66000HepG2SRFBP1
CPSF3ENSG00000119203.91027.692301394.98990-0.440802.773701.77100HepG2SRSF3
CPSF3ENSG00000119203.91658.228002080.31350-0.327204.528303.76160HepG2SRSF5
CPSF3ENSG00000119203.9981.978401713.20690-0.8029020.8175019.23560HepG2SRSF7
CPSF3ENSG00000119203.91607.476102005.03920-0.318804.749504.11330HepG2SSB
CPSF3ENSG00000119203.92064.441802365.83820-0.196602.333701.75310HepG2SUCLG1
CPSF3ENSG00000119203.9735.04690994.79590-0.436603.776802.69140HepG2SUPT6H
CPSF3ENSG00000119203.9830.079401319.07760-0.668205.990805.05250HepG2SUPV3L1
CPSF3ENSG00000119203.91760.194601377.984000.353104.183303.51550HepG2TAF15
CPSF3ENSG00000119203.9718.513001276.68590-0.8293011.312009.99600HepG2TARDBP
CPSF3ENSG00000119203.9739.668601367.29680-0.8864017.4237016.36510HepG2TIAL1
CPSF3ENSG00000119203.91032.133501379.63380-0.418706.315905.52610HepG2TRIM56
CPSF3ENSG00000119203.91514.659702058.43060-0.442605.176803.94040HepG2TUFM
CPSF3ENSG00000119203.9475.77010779.23680-0.711806.554905.37670HepG2UCHL5
CPSF3ENSG00000119203.91033.372001278.77390-0.307403.602402.82120HepG2UPF1
CPSF3ENSG00000119203.9916.319601234.60220-0.430106.019905.19440HepG2UTP3
CPSF3ENSG00000119203.91117.395501406.40310-0.331904.961204.28210HepG2ZNF622
CPSF3ENSG00000119203.92139.413302433.02900-0.185502.095201.58910K562AGGF1
CPSF3ENSG00000119203.92014.988402531.63250-0.329303.118502.42390K562AKAP8L
CPSF3ENSG00000119203.91426.982803233.58970-1.1802028.0436026.37750K562AQR
CPSF3ENSG00000119203.91547.683202007.92230-0.375606.105404.66040K562BCLAF1
CPSF3ENSG00000119203.91031.799601511.40250-0.550705.576904.32840K562BOP1
CPSF3ENSG00000119203.91709.916002252.73180-0.397803.115901.59230K562BUD13
CPSF3ENSG00000119203.92019.552102825.19870-0.484303.455201.81710K562CKAP4
CPSF3ENSG00000119203.91824.899602646.38200-0.536202.849401.76740K562CNOT7
CPSF3ENSG00000119203.91072.863201607.05730-0.583007.948106.60310K562CPSF6
CPSF3ENSG00000119203.91277.780901523.30820-0.253602.357401.39540K562CSTF2
CPSF3ENSG00000119203.94496.746005300.62000-0.237302.506601.57850K562CELF1
CPSF3ENSG00000119203.91752.328402224.06480-0.343904.399202.85140K562DDX21
CPSF3ENSG00000119203.91089.407801432.74310-0.395203.876902.61480K562DDX3X
CPSF3ENSG00000119203.91161.723101452.61730-0.322403.389701.90420K562DDX6
CPSF3ENSG00000119203.91102.014801778.47390-0.690504.389803.22260K562EFTUD2
CPSF3ENSG00000119203.92216.100702642.15510-0.253702.926302.19050K562EIF2S2
CPSF3ENSG00000119203.91172.506901904.64820-0.699903.824102.58640K562EIF3D
CPSF3ENSG00000119203.93323.748804310.99270-0.375206.513305.09260K562EIF4G2
CPSF3ENSG00000119203.91295.409001702.49690-0.394204.106302.52870K562EXOSC5
CPSF3ENSG00000119203.91036.539201635.13730-0.657608.081806.57330K562FMR1
CPSF3ENSG00000119203.91020.533101385.92400-0.441503.425602.39990K562FTO
CPSF3ENSG00000119203.91877.322301556.684700.270103.000402.37370K562FXR1
CPSF3ENSG00000119203.91956.873202314.39170-0.242102.489701.41240K562GLRX3
CPSF3ENSG00000119203.91049.659901534.34640-0.547706.358205.15630K562GPKOW
CPSF3ENSG00000119203.91945.246603521.04880-0.8561018.9802016.92310K562GRSF1
CPSF3ENSG00000119203.91839.060802356.29460-0.357603.950002.67000K562HNRNPA1
CPSF3ENSG00000119203.91392.892301953.28240-0.487805.947305.10500K562HNRNPC
CPSF3ENSG00000119203.92609.101202028.475700.363102.939301.66540K562HNRNPK
CPSF3ENSG00000119203.91565.266302030.20380-0.375202.438001.49300K562IGF2BP2
CPSF3ENSG00000119203.9845.313701310.13470-0.632204.869003.58920K562KRR1
CPSF3ENSG00000119203.91523.264201980.74100-0.378902.889701.39800K562LIN28B
CPSF3ENSG00000119203.91119.993101497.69240-0.419304.239603.14110K562METAP2
CPSF3ENSG00000119203.93303.834004595.10040-0.476005.660404.04870K562MSI2
CPSF3ENSG00000119203.91613.105602433.27520-0.5931015.1143013.41300K562MTPAP
CPSF3ENSG00000119203.91905.220502703.62040-0.5049016.4312014.81980K562NSUN2
CPSF3ENSG00000119203.91487.649601922.95330-0.370302.693201.30130K562NUSAP1
CPSF3ENSG00000119203.91425.372101899.12670-0.414004.228903.01320K562PCBP2
CPSF3ENSG00000119203.91154.508101751.27880-0.601107.762806.09690K562PSIP1
CPSF3ENSG00000119203.94114.697204901.99670-0.252603.278802.23230K562PUM2
CPSF3ENSG00000119203.91727.327302511.00310-0.539706.241505.46550K562PUS1
CPSF3ENSG00000119203.91945.939902446.33040-0.330204.269603.54850K562RBM15
CPSF3ENSG00000119203.91500.155901988.65830-0.406703.936902.92020K562RBM22
CPSF3ENSG00000119203.91252.039701597.60570-0.351603.351602.26060K562RCC2
CPSF3ENSG00000119203.92167.115302667.73400-0.299804.033403.05710K562SF3A3
CPSF3ENSG00000119203.91057.256201459.20990-0.464903.534402.42940K562SF3B1
CPSF3ENSG00000119203.9814.719201058.93540-0.378202.636701.40480K562SLBP
CPSF3ENSG00000119203.91139.792201514.50920-0.410103.697602.46340K562SRFBP1
CPSF3ENSG00000119203.91392.845102032.71610-0.545407.775006.59550K562SRSF1
CPSF3ENSG00000119203.91514.756201919.56750-0.341702.816301.75500K562SRSF5
CPSF3ENSG00000119203.91426.442501984.60190-0.476407.802305.84340K562SRSF7
CPSF3ENSG00000119203.91092.862901676.21430-0.617103.436602.29200K562SUPV3L1
CPSF3ENSG00000119203.91586.893002057.39780-0.374603.153802.39800K562TARDBP
CPSF3ENSG00000119203.91034.296301684.46270-0.703608.114406.44400K562TIAL1
CPSF3ENSG00000119203.91163.358801789.29020-0.621108.083806.26830K562TRIM56
CPSF3ENSG00000119203.92565.287802991.81040-0.221902.928701.62170K562TROVE2
CPSF3ENSG00000119203.91254.116501773.78010-0.500202.430301.48280K562UCHL5
CPSF3ENSG00000119203.92089.716402866.70340-0.4561010.571309.28050K562UPF1
CPSF3ENSG00000119203.91749.549202452.95190-0.487506.636805.24720K562WDR3
CPSF3ENSG00000119203.92521.899003642.83410-0.530607.440205.90660K562ZC3H8
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 CPSF3 is not available on ENCORE database.





4 RBPs can affect the splicing of CPSF3 :

Event TypeGene NameGene IDchrStrandExonStartExonEnd2ndExonStart2ndExonEndupstreamESupstreamEEdownstreamESdownstreamEEdPSIp-valueFDRis_includedCell LineAffected by RBPBound by RBP
SECPSF3ENSG00000119203.9chr2+957088095710099570051957014995726399572817-0.076000.000290.00761excludedK562SF3B4
SECPSF3ENSG00000119203.9chr2+957088095710099570051957014995726399572817-0.087000.000110.00350excludedK562U2AF1
SECPSF3ENSG00000119203.9chr2+9581663958173095806199580795958194695821050.094000.000240.09834includedHepG2GRSF1
SECPSF3ENSG00000119203.9chr2+957088095710099570051957014995726399572817-0.081000.000010.00088excludedK562TARDBP

*: "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 CPSF3 is not avaliable on ENCORE database.