CTCF

General Information

Gene Name       : CTCF
Gene ID             : ENSG00000102974.15
Essential Gene : Yes

Functions

Localization

Domains (AlphaFold: CTCF)


Antibody Validation

 View validation images for all CTCF antibodies

Expression Level in Cell lines

Cell Line Gene Name Ensembl ID Rep1 TPM Rep2 TPM Average TPM Experiment ID
Gm12878CTCFENSG00000102974.1533.3437.4335.39ENCSR000AEF
HepG2CTCFENSG00000102974.1541.6450.5946.12ENCSR985KAT
K562CTCFENSG00000102974.1529.6231.7030.66ENCSR000AEO

Assays

2 Released experiments are available on ENCORE database.

Assay TypeExp_NameENCODE IDTarget labelBiosampleStatusLinked AntibodyControlsMethodNote
knockdown followed by RNA-seq CTCF-BGKcLV17-K562ENCSR613LSQCTCFK562ReleasedENCSR516TLX   CRISPRKD% = 61.4,69
knockdown followed by RNA-seq CTCF-BGHcLV18-HepG2ENCSR871XPXCTCFHepG2ReleasedENCSR670KAS   CRISPRKD% = 70.2,69.5






  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  
CTCFENCAB363WCMPA5-17143UC2731408NotSatisfied, ENCODE4BGHcLV18-5, Released, ENCODE4BGKcLV17-5, Released, ENCODE4
CTCF3418S5Submitted, ENCORE2BGHcLV18-5, Submitted, ENCORE2


  KD RNA-Seq  
  GeneName    Cell_Line    Method    Exp_ID    Control_ID    Sample_reps    Control_reps    KD%    Status    Project    Note  
CTCFK562CRISPRENCSR613LSQENCSR516TLXCTCF-BGKcLV17-5,CTCF-BGKcLV17-6NT-BGKcLV17-1,NT-BGKcLV17-261.4,69ReleasedENCODE4
CTCFHepG2CRISPRENCSR871XPXENCSR670KASCTCF-BGHcLV18-5,CTCF-BGHcLV18-6NT-BGHcLV18-1,NT-BGHcLV18-270.2,69.5ReleasedENCODE4
CTCFRibo-STAMP-293TshRNABGRSLV10-7,BGRSLV10-8BGRSLV10-1,BGRSLV10-2NotSatisfiedENCORE2
CTCFRibo-STAMP-293TshRNABGRSLV10-9,BGRSLV10-10BGRSLV10-1,BGRSLV10-2NotSatisfiedENCORE2
CTCFRibo-STAMP-293TshRNABGRSDLV02-21,BGRSDLV02-22BGRSDLV02-1,BGRSDLV02-2SubmittedENCORE2
CTCFRibo-STAMP-293TshRNACTCF-BGRSDLV02-23dox,CTCF-BGRSDLV02-24doxCTCF-BGRSDLV02-21,CTCF-BGRSDLV02-22,SubmittedENCORE2


  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
CTCFProduct_ID: PA5-17143
Lot_ID: UC2731408
Source: Thermo Fisher
Target Name: CTCF-human		 CTCF-HepG2-CRISPR-PA5-17143.png<br>Caption: Western blot following CRISPR against CTCF in HepG2 whole cell lysate using CTCF specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CTCF. CTCF protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
 ThermoFisher_PA5-17143_UC2731408_CTCF.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the CTCF specific antibody, PA5-17143. 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 CTCF-specific antibody, PA5-17143. 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.
 CTCF-K562-CRISPR-PA5-17143.png<br>Caption: Western blot following CRISPR against CTCF in K562 whole cell lysate using CTCF specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CTCF. CTCF protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
CTCFProduct_ID: 3418S
Lot_ID: 5
Source: Cell Signaling Technology
Target Name: CTCF-human		 CTCF-HEPG2-CRISPR-3418S.png<br>Caption: Western blot following CRISPR against CTCF in HepG2 whole cell lysate using CTCF specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CTCF. CTCF protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_3418S_5_CTCF.png<br>Caption: IP-WB analysis of 3418S whole cell lysate using the CTCF specific antibody, 3418S. 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 CTCF-specific antibody, 3418S. 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 CTCF is not avaliable on ENCORE database.



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







eCLIP assay for CTCF is not avaliable on ENCORE database.





24 proteins are bound to CTCF RNA:

Chr Start End Strand Matched Area log2(fold change) -log(p-value) Cell Line Binding Protein Name
chr166767226967672353+3'-UTR4.7772016.45754K562PUM2
chr166767184367671904+3'-UTR4.320054.97297K562TIA1
chr166767248367672550+3'-UTR3.427143.34573K562IGF2BP2
chr166767287367672919+3'-UTR3.120623.90824K562YBX3
chr166765059867650701+3'-UTR,CDS,intron-Proximal5.7466410.40229HepG2U2AF2
chr166759646167596628+5'-UTR,intron-Proximal3.325108.57919HepG2NCBP2
chr166759646867596623+5'-UTR3.9650911.61348K562DDX3X
chr166759652867596628+5'-UTR,intron-Proximal5.484318.83919K562FXR2
chr166759649167596586+5'-UTR3.5210510.24163HepG2DDX3X
chr166759649967596636+5'-UTR,intron-Proximal3.072395.33097HepG2SRSF1
chr166766341367663437+CDS,intron-Proximal3.248653.07653K562ZNF622
chr166767060367670695+CDS3.744027.65528K562ZNF622
chr166764514267645215+CDS,intron-Distal3.347658.16183HepG2BCLAF1
chr166767063967670696+CDS3.507034.49347K562UCHL5
chr166764493667645013+CDS,intron-Distal3.515933.86355HepG2PPIG
chr166767075167670833+CDS,intron-Proximal5.858799.41643K562AQR
chr166766337267663439+CDS,intron-Proximal3.539306.18248K562UCHL5
chr166764481867644899+CDS,intron-Distal5.139558.77129K562UCHL5
chr166766332467663427+CDS3.545154.31813HepG2G3BP1
chr166764510267645222+CDS,intron-Distal3.399784.24058K562GRWD1
chr166764480367644895+CDS,intron-Distal4.184616.16300K562FMR1
chr166764516867645242+CDS,intron-Distal3.905205.77244K562UCHL5
chr166767059067670624+CDS,intron-Proximal3.916746.11943K562UCHL5
chr166767064667670716+CDS3.383477.01246HepG2BCLAF1
chr166765070567650778+CDS3.140033.09129HepG2GRWD1
chr166764477767644882+CDS,intron-Distal4.562377.57065K562FXR2
chr166764595767645977+CDS,intron-Distal3.867413.34184HepG2GRWD1
chr166764540067645491+CDS,intron-Distal5.515528.86847HepG2BCLAF1
chr166766343267663493+CDS,intron-Proximal4.747594.13847K562AQR
chr166764501167645143+CDS,intron-Distal5.5493010.55912K562PUM2
chr166764491667644986+CDS,intron-Distal3.706654.41784HepG2GRWD1
chr166764493367644944+CDS,intron-Distal4.220393.02457HepG2BCLAF1
chr166764600067646017+CDS,intron-Distal3.051104.14323K562YBX3
chr166767059167670743+CDS,intron-Proximal3.957739.61128K562ZNF800
chr166764476067644875+CDS,intron-Distal3.286996.07026HepG2GRWD1
chr166762562767625688+intron-Distal3.264164.15830HepG2ILF3
chr166764557967645675+intron-Distal,intron-Proximal4.023434.07352K562KHSRP
chr166761774867617840+intron-Distal4.301514.07991K562ILF3
chr166761226067612309+intron-Distal3.143403.29440K562ILF3
chr166759712467597205+intron-Distal4.0565816.24146HepG2XPO5
chr166766771967667772+intron-Distal4.199663.86413K562AGGF1
chr166761412667614218+intron-Distal3.823613.75100HepG2STAU2
chr166760519567605259+intron-Proximal3.188853.15050HepG2TIAL1
ChrStartEndStrandMatched Arealog2(fold change)-log(p-value)Cell LineBinding Protein Name




eCLIP assay for CTCF is not avaliable on ENCORE database.



Diffrential Expression

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

  • 76 RBPs can affect the levels of CTCF.  








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





76 RBPs can affect the gene expression of CTCF :

Gene NameGene IDKDMeanCNMeanlog2(fold change) *-log(pval) **-log(padj) **Cell LineAffected by RBPBound by RBP
CTCFENSG00000102974.101909.139802322.27510-0.282603.794803.01350HepG2AUH
CTCFENSG00000102974.101056.928701373.98960-0.378502.406101.56990HepG2BCLAF1
CTCFENSG00000102974.101765.388002944.63190-0.7381012.2515011.11420HepG2BOP1
CTCFENSG00000102974.101583.308401863.43250-0.235002.069101.39550HepG2CALR
CTCFENSG00000102974.101382.571602703.38610-0.9674018.1881016.60840HepG2CPSF6
CTCFENSG00000102974.101081.836701306.07280-0.271801.919801.34250HepG2DDX21
CTCFENSG00000102974.101321.852301643.25080-0.314001.960401.42520HepG2DDX3X
CTCFENSG00000102974.101112.299501554.71410-0.483103.556702.69390HepG2DDX55
CTCFENSG00000102974.101005.716801411.41810-0.488903.566502.87310HepG2DDX6
CTCFENSG00000102974.101061.176801255.65850-0.242802.084901.46560HepG2DNAJC21
CTCFENSG00000102974.10966.817801244.50790-0.364305.444504.57530HepG2DNAJC2
CTCFENSG00000102974.101908.109701387.748500.459304.224803.10860HepG2EEF2
CTCFENSG00000102974.101066.326801356.99750-0.347802.257101.71670HepG2EIF2S1
CTCFENSG00000102974.101547.493001126.549000.457903.859802.80300HepG2EIF3D
CTCFENSG00000102974.101918.945601460.036200.394202.225201.60470HepG2EIF4B
CTCFENSG00000102974.101714.795202019.46210-0.235902.326501.54700HepG2EIF4G1
CTCFENSG00000102974.101692.388102707.90820-0.678102.870701.83580HepG2FTO
CTCFENSG00000102974.101925.818703064.64580-0.670207.696206.66250HepG2GPKOW
CTCFENSG00000102974.101604.614401881.22350-0.229402.352301.48250HepG2HNRNPA2B1
CTCFENSG00000102974.101622.570002179.29280-0.425607.245206.15590HepG2HNRNPF
CTCFENSG00000102974.101303.094201864.62960-0.5169012.3222010.99410HepG2HNRNPL
CTCFENSG00000102974.101729.785302924.63460-0.7577011.104109.94620HepG2HNRNPLL
CTCFENSG00000102974.101762.746902145.99220-0.283802.594501.89310HepG2IGF2BP1
CTCFENSG00000102974.101099.271101426.75110-0.376202.575301.92180HepG2IGF2BP2
CTCFENSG00000102974.101190.571501430.79900-0.265203.233002.44590HepG2ILF2
CTCFENSG00000102974.102020.496401513.439800.416803.322402.60340HepG2MAGOH
CTCFENSG00000102974.102096.577202982.42590-0.508503.365802.28920HepG2MTPAP
CTCFENSG00000102974.102060.809002593.14120-0.331502.842302.08310HepG2NSUN2
CTCFENSG00000102974.101047.672901249.33940-0.254002.230201.56150HepG2PPIL4
CTCFENSG00000102974.10926.301901199.32390-0.372702.437401.67730HepG2PRPF8
CTCFENSG00000102974.101520.254301937.59300-0.350003.289102.64730HepG2PUF60
CTCFENSG00000102974.101973.291101609.825700.293603.518202.92400HepG2NELFE
CTCFENSG00000102974.101756.100701499.286900.228002.302001.73300HepG2RECQL
CTCFENSG00000102974.101089.019401487.91700-0.450302.416701.53300HepG2RPS10
CTCFENSG00000102974.102170.632402894.89540-0.415402.816402.10370HepG2SF3B1
CTCFENSG00000102974.101585.357201857.85180-0.228802.896602.18010HepG2SLBP
CTCFENSG00000102974.101661.008401454.724200.191202.140101.56260HepG2SMN1
CTCFENSG00000102974.102241.267503221.04830-0.523203.310702.45230HepG2SNRNP70
CTCFENSG00000102974.102093.484802517.01610-0.265803.750703.19430HepG2SRFBP1
CTCFENSG00000102974.102438.753101571.950900.6335016.7796015.82360HepG2SRSF1
CTCFENSG00000102974.101698.711702141.04550-0.333904.677603.80810HepG2SRSF7
CTCFENSG00000102974.101051.311701547.69030-0.557904.788003.93530HepG2SUPV3L1
CTCFENSG00000102974.101204.623301412.86750-0.230002.002701.51290HepG2TAF15
CTCFENSG00000102974.101391.974202850.22350-1.0339021.4983019.83940HepG2TARDBP
CTCFENSG00000102974.10922.895301361.14520-0.560607.598006.84420HepG2TIAL1
CTCFENSG00000102974.10990.330201373.22910-0.471607.756906.89010HepG2TRIM56
CTCFENSG00000102974.102787.128101843.029100.596607.432306.40940HepG2U2AF1
CTCFENSG00000102974.101552.873902003.65680-0.367702.618701.80440HepG2UBE2L3
CTCFENSG00000102974.10573.59430914.26590-0.672606.402605.24220HepG2UCHL5
CTCFENSG00000102974.101422.235101947.11890-0.453208.891707.75990HepG2UPF1
CTCFENSG00000102974.101230.333701523.53150-0.308401.942201.32710HepG2XRN2
CTCFENSG00000102974.101554.751501768.06120-0.185501.991801.40790HepG2ZC3H8
CTCFENSG00000102974.101589.679002141.45390-0.429909.984509.10750HepG2ZNF622
CTCFENSG00000102974.101880.181801461.222600.363605.377304.62800K562AGGF1
CTCFENSG00000102974.102542.909502037.333900.319702.603502.03010K562AQR
CTCFENSG00000102974.101430.391701746.26160-0.287902.611301.47670K562CCDC124
CTCFENSG00000102974.101134.758001911.32080-0.7522010.351008.82050K562CPSF6
CTCFENSG00000102974.101736.378501253.849500.469603.272901.87080K562EEF2
CTCFENSG00000102974.101833.565601297.086200.499303.231002.10680K562EIF3D
CTCFENSG00000102974.103228.410202737.144500.238103.265502.24790K562EIF4G2
CTCFENSG00000102974.101572.572301944.62220-0.306402.351601.56140K562FMR1
CTCFENSG00000102974.101285.272001648.19870-0.358802.643501.75060K562FTO
CTCFENSG00000102974.101520.930901124.816100.435206.302905.44450K562FXR1
CTCFENSG00000102974.101436.485801824.88290-0.345303.043902.21200K562GPKOW
CTCFENSG00000102974.101798.470802429.47640-0.433905.102904.07470K562GRSF1
CTCFENSG00000102974.101068.344801378.59340-0.367803.251802.61260K562HNRNPC
CTCFENSG00000102974.102268.021202739.41640-0.272402.087001.39300K562HSPD1
CTCFENSG00000102974.101181.632101558.11260-0.399002.275401.43750K562KRR1
CTCFENSG00000102974.102229.241301807.650300.302302.691001.79790K562MBNL1
CTCFENSG00000102974.101332.126901781.27170-0.419204.319503.20930K562METAP2
CTCFENSG00000102974.102234.070702917.58160-0.385103.532602.25550K562MSI2
CTCFENSG00000102974.101622.631002087.18240-0.363202.693301.87370K562PCBP3
CTCFENSG00000102974.101193.495501600.92410-0.423704.754103.70330K562POLR2G
CTCFENSG00000102974.101845.430502293.73760-0.313702.505701.72970K562PPIG
CTCFENSG00000102974.101696.990201178.886100.525505.329104.28740K562PRPF8
CTCFENSG00000102974.10874.263801236.04580-0.499605.042003.77210K562PSIP1
CTCFENSG00000102974.101932.527501507.926300.357803.013302.45040K562PUS1
CTCFENSG00000102974.102228.560101469.209600.6010011.4040010.21840K562RBM15
CTCFENSG00000102974.10866.246601127.69520-0.380503.441202.34010K562RCC2
CTCFENSG00000102974.10820.808701200.81680-0.548904.295703.27480K562RPS19
CTCFENSG00000102974.101746.256601426.512200.291702.389601.38770K562SAFB
CTCFENSG00000102974.102210.485401605.790700.461006.389105.13430K562SYNCRIP
CTCFENSG00000102974.10879.905001188.87380-0.434203.202802.19030K562TIAL1
CTCFENSG00000102974.101848.413002212.87240-0.259603.151102.38740K562UPF1
CTCFENSG00000102974.101860.097902295.08650-0.303202.603101.77130K562ZC3H8
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 CTCF is not available on ENCORE database.





3 RBPs can affect the splicing of CTCF :

Event TypeGene NameGene IDchrStrandExonStartExonEnd2ndExonStart2ndExonEndupstreamESupstreamEEdownstreamESdownstreamEEdPSIp-valueFDRis_includedCell LineAffected by RBPBound by RBP
SECTCFENSG00000102974.10chr16+676458536764602467644726676455166765064767650781-0.062000.000140.00234excludedK562AQR
SECTCFENSG00000102974.10chr16+676458536764602467605050676051676765064767650781-0.090000.000700.01265excludedK562PUS1
A3SSCTCFENSG00000102974.10chr16+6766326767663436676633006766343667662272676624550.100000.000000.00000longerK562AQR
A3SSCTCFENSG00000102974.10chr16+6764582667646024676458536764602467644726676455160.092000.000000.00000longerK562AQR
MXECTCFENSG00000102974.10chr16+6764472667645516676458536764602467605050676051676765064767650781-0.145000.000070.007082includedK562SAFB

*: "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 CTCF is not avaliable on ENCORE database.