SCN1A

General Information

Gene Name       : SCN1A
Gene ID             : ENSG00000144285.19
Essential Gene : No

Functions

Localization

Domains (AlphaFold: SCN1A)


Antibody Validation

Expression Level in Cell lines

Cell Line Gene Name Ensembl ID Rep1 TPM Rep2 TPM Average TPM Experiment ID
Gm12878SCN1AENSG00000144285.190.000.000.00ENCSR000AEF
HepG2SCN1AENSG00000144285.197.9614.8011.38ENCSR985KAT
K562SCN1AENSG00000144285.190.000.000.00ENCSR000AEO

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 SCN1A is not avaliable on ENCORE database.



Proteins bound to RNA
  • SCN1A RNA is bound by 16 proteins.  







eCLIP assay for SCN1A is not avaliable on ENCORE database.





16 proteins are bound to SCN1A RNA:

Chr Start End Strand Matched Area log2(fold change) -log(p-value) Cell Line Binding Protein Name
chr2166846238166846312-3'-UTR,intron-Distal3.156893.38928HepG2ZC3H11A
chr2166930116166930147-5'-UTR,CDS,intron-Distal,intron-Proximal3.895366.81385HepG2BCLAF1
chr2166894291166894333-CDS,intron-Distal4.763524.29511HepG2EIF3H
chr2166892803166892868-CDS,intron-Distal3.638716.91872HepG2BCLAF1
chr2166908366166908405-CDS,intron-Distal4.496787.97334HepG2BCLAF1
chr2166929883166929927-CDS,intron-Distal4.576309.47159HepG2BCLAF1
chr2166892977166893012-CDS,intron-Distal3.135856.09950HepG2BCLAF1
chr2166894481166894534-CDS,intron-Distal3.790146.62597HepG2GRWD1
chr2166900210166900296-CDS,intron-Distal,intron-Proximal4.090316.39499HepG2GRWD1
chr2166897945166897979-CDS,intron-Distal3.633949.41803HepG2BCLAF1
chr2166866290166866346-CDS,intron-Distal3.000164.91547HepG2GRWD1
chr2166856233166856263-CDS,intron-Distal3.810059.50935HepG2BCLAF1
chr2166898816166898875-CDS,intron-Distal3.333086.81726HepG2GRWD1
chr2166892567166892605-CDS,intron-Distal3.308187.33138HepG2BCLAF1
chr2166911146166911206-CDS,intron-Distal,intron-Proximal3.8925314.94623HepG2BCLAF1
chr2166872116166872127-CDS,intron-Distal,intron-Proximal5.012877.04013HepG2BCLAF1
chr2166854564166854569-CDS,intron-Distal,intron-Proximal4.012874.09885HepG2BCLAF1
chr2166897839166897885-CDS,intron-Distal6.0803413.95734HepG2BCLAF1
chr2166866289166866334-CDS,intron-Distal3.760378.25092HepG2BCLAF1
chr2166894448166894481-CDS,intron-Distal4.033764.23295HepG2GRWD1
chr2166908318166908361-CDS,intron-Distal3.961596.39464HepG2BCLAF1
chr2166854663166854685-CDS,intron-Distal3.761625.97823HepG2BCLAF1
chr2166900332166900399-CDS,intron-Distal4.0075515.57800HepG2BCLAF1
chr2166912994166913008-CDS,intron-Distal4.305356.22576HepG2BCLAF1
chr2166905394166905443-CDS,intron-Distal,intron-Proximal4.2831517.28671HepG2BCLAF1
chr2166897885166897921-CDS,intron-Distal4.8981311.54096HepG2BCLAF1
chr2166856231166856287-CDS,intron-Distal,intron-Proximal3.084685.14343HepG2PPIG
chr2166901812166901835-CDS,intron-Distal3.698833.12746HepG2GRWD1
chr2166904242166904279-CDS,intron-Distal,intron-Proximal3.7737915.36859HepG2BCLAF1
chr2166898818166898869-CDS,intron-Distal3.475093.34034HepG2HLTF
chr2166903351166903417-CDS,intron-Distal3.171615.59833HepG2GRWD1
chr2166905394166905434-CDS,intron-Distal,intron-Proximal4.873386.20441HepG2HLTF
chr2166903280166903322-CDS,intron-Distal4.9840211.09109HepG2BCLAF1
chr2166915093166915129-CDS,intron-Distal4.550767.53358HepG2BCLAF1
chr2166900525166900555-CDS,intron-Distal6.0137613.92749HepG2BCLAF1
chr2166929878166929919-CDS,intron-Distal3.895256.62597HepG2GRWD1
chr2166900337166900442-CDS,intron-Distal3.421644.59965HepG2PRPF4
chr2166912921166912994-CDS,intron-Distal3.6995312.42637HepG2BCLAF1
chr2166900222166900261-CDS,intron-Distal,intron-Proximal3.220396.80151HepG2BCLAF1
chr2166901609166901637-CDS,intron-Distal3.706116.81385HepG2BCLAF1
chr2166911148166911203-CDS,intron-Distal4.625565.59408HepG2GRWD1
chr2166901663166901732-CDS,intron-Distal3.356076.68812HepG2BUD13
chr2166908451166908495-CDS,intron-Distal3.448416.50801HepG2BCLAF1
chr2166900352166900476-CDS,intron-Distal3.3664410.78389HepG2GRWD1
chr2166909412166909446-CDS,intron-Distal3.657478.74800HepG2BCLAF1
chr2166898815166898880-CDS,intron-Distal3.098248.11238HepG2BCLAF1
chr2166898801166898815-CDS,intron-Distal,intron-Proximal3.283825.40132HepG2BCLAF1
chr2166900306166900343-CDS,intron-Distal4.178044.01763HepG2GRWD1
chr2166850812166850905-CDS,intron-Distal4.730904.91614HepG2GRWD1
chr2166866230166866290-CDS,intron-Distal3.098685.33987HepG2GRWD1
chr2166903357166903437-CDS,intron-Distal4.0678715.02931HepG2BCLAF1
chr2166901553166901577-CDS,intron-Distal4.7413010.13662HepG2BCLAF1
chr2166870364166870406-CDS,intron-Distal3.761627.83567HepG2BCLAF1
chr2166940390166940557-intron-Distal4.058934.21977HepG2HNRNPL
chr2166910885166910934-intron-Distal4.227838.73821HepG2HNRNPL
chr2166872504166872573-intron-Distal4.083307.02083HepG2PTBP1
chr2166928940166929018-intron-Distal3.955773.64762HepG2QKI
chr2166873290166873374-intron-Distal3.480724.31768HepG2KHSRP
chr2166984057166984154-intron-Distal4.754088.48623HepG2PCBP2
chr2166964810166964876-intron-Distal4.718803.50357HepG2QKI
chr2166929785166929839-intron-Distal,intron-Proximal4.552655.39405HepG2RBM22
chr2166910829166910923-intron-Distal3.009483.14777HepG2GTF2F1
chr2166864462166864532-intron-Distal4.954966.12104HepG2QKI
chr2166877711166877835-intron-Distal4.4989310.10565HepG2QKI
chr2166924301166924377-intron-Distal3.265653.01092HepG2LIN28B
chr2166965123166965172-intron-Distal4.300793.16986HepG2QKI
chr2166910830166910877-intron-Distal3.484156.53997HepG2HNRNPL
chr2166865884166865943-intron-Distal3.943344.79415HepG2KHSRP
chr2166919910166919955-intron-Distal3.406003.64762HepG2QKI
chr2166914891166914966-intron-Distal3.221413.02891HepG2HNRNPL
chr2166917689166917834-intron-Distal3.045704.37687HepG2PTBP1
chr2166865616166865667-intron-Distal3.525973.94088HepG2QKI
chr2166910877166910885-intron-Distal3.713176.22956HepG2HNRNPL
chr2166856420166856502-intron-Distal3.154683.29213HepG2KHSRP
chr2166970747166970874-intron-Distal3.897973.27714HepG2HNRNPL
chr2166865943166866024-intron-Distal3.740074.54121HepG2KHSRP
chr2166865779166865884-intron-Distal4.331505.56216HepG2KHSRP
chr2166910442166910547-intron-Distal5.052048.54919HepG2PTBP1
ChrStartEndStrandMatched Arealog2(fold change)-log(p-value)Cell LineBinding Protein Name




eCLIP assay for SCN1A is not avaliable on ENCORE database.



Diffrential Expression

  • The Knockdown/knockout assay for SCN1A is not available on ENCORE database.

  • 120 RBPs can affect the levels of SCN1A.  








The Knockdown/knockout RNA-Seq assay for SCN1A is not available on ENCORE database.





120 RBPs can affect the gene expression of SCN1A :

Gene NameGene IDKDMeanCNMeanlog2(fold change) *-log(pval) **-log(padj) **Cell LineAffected by RBPBound by RBP
SCN1AENSG00000144285.11610.09340859.99670-0.495304.200002.90800HepG2AATF
SCN1AENSG00000144285.111773.542301386.860100.354702.543701.63890HepG2ABCF1
SCN1AENSG00000144285.11969.221901238.24130-0.353403.132402.49190HepG2ACO1
SCN1AENSG00000144285.111653.72550646.729301.3544011.9281010.06390HepG2ADAR
SCN1AENSG00000144285.11451.828901189.75260-1.3968020.2913018.98750HepG2AKAP1
SCN1AENSG00000144285.11421.260501284.40510-1.6083028.3868025.51920HepG2AKAP8
SCN1AENSG00000144285.111119.22100705.900100.664906.579005.25710HepG2BCLAF1
SCN1AENSG00000144285.11118.76280835.03620-2.8138050.7710048.83960HepG2BOP1
SCN1AENSG00000144285.111356.990801039.286500.384703.844602.40380HepG2BUD13
SCN1AENSG00000144285.11623.62220926.26120-0.570706.482705.36600HepG2CALR
SCN1AENSG00000144285.112847.050801089.527901.3857022.8138020.25710HepG2CCAR1
SCN1AENSG00000144285.111851.399401238.169300.5803014.8452013.55930HepG2CKAP4
SCN1AENSG00000144285.11961.39390766.582800.326601.986601.39350HepG2CPSF6
SCN1AENSG00000144285.111204.68290501.841601.2632024.1626021.62470HepG2CSTF2
SCN1AENSG00000144285.11545.092001135.98990-1.0594016.9552015.63480HepG2CELF1
SCN1AENSG00000144285.11715.837701221.75110-0.771209.852808.59220HepG2DAZAP1
SCN1AENSG00000144285.112587.258301145.286401.1756061.0946058.53120HepG2DDX19B
SCN1AENSG00000144285.111462.82500928.491400.655709.521507.86140HepG2DDX24
SCN1AENSG00000144285.11832.07080605.124500.459403.084801.60910HepG2DDX28
SCN1AENSG00000144285.11442.100701139.73650-1.3663022.1752020.58440HepG2DDX3X
SCN1AENSG00000144285.11479.87580798.66100-0.734905.463504.42200HepG2DDX55
SCN1AENSG00000144285.111748.54850870.519701.006103.064502.03660HepG2DDX59
SCN1AENSG00000144285.112072.798001282.339000.692704.343503.08590HepG2DDX5
SCN1AENSG00000144285.11904.07870628.106500.525304.922503.63200HepG2DHX30
SCN1AENSG00000144285.111770.189701184.712300.5793011.6704010.47910HepG2DKC1
SCN1AENSG00000144285.11328.61240651.22600-0.9868015.1285013.60140HepG2DNAJC21
SCN1AENSG00000144285.111032.75970645.473400.6780014.1212012.76380HepG2DNAJC2
SCN1AENSG00000144285.111303.34990964.952900.433602.710701.79800HepG2EEF2
SCN1AENSG00000144285.111445.90850941.194600.619306.123005.25930HepG2EIF2S1
SCN1AENSG00000144285.11286.29900783.34180-1.4521019.8426017.69420HepG2EIF3D
SCN1AENSG00000144285.111483.262501040.179800.511804.104203.32940HepG2EIF4A3
SCN1AENSG00000144285.11678.182201012.66730-0.578403.585702.80720HepG2EIF4B
SCN1AENSG00000144285.112980.657601201.548701.3106033.9091030.94950HepG2ESF1
SCN1AENSG00000144285.113629.207402655.605500.450509.933708.90900HepG2ETF1
SCN1AENSG00000144285.11679.759601210.15790-0.8321011.164609.51510HepG2EWSR1
SCN1AENSG00000144285.11666.54100904.14330-0.439903.703002.40790HepG2FASTKD2
SCN1AENSG00000144285.11258.239701400.45260-2.4391057.9948055.40030HepG2FIP1L1
SCN1AENSG00000144285.111057.51790627.159600.7537010.024208.57460HepG2FUBP3
SCN1AENSG00000144285.11793.288801049.34920-0.403602.780402.08700HepG2FXR1
SCN1AENSG00000144285.11740.38250973.50340-0.394902.435401.80920HepG2G3BP1
SCN1AENSG00000144285.112066.675101033.396500.9998016.5994014.46920HepG2G3BP2
SCN1AENSG00000144285.111003.84610697.469200.525204.402703.26360HepG2GEMIN5
SCN1AENSG00000144285.111388.52570930.367400.577604.694502.31880HepG2GRWD1
SCN1AENSG00000144285.11594.714001121.96200-0.915807.500205.11570HepG2GTF2F1
SCN1AENSG00000144285.111105.64550731.307500.596206.178205.17360HepG2HNRNPC
SCN1AENSG00000144285.111473.91100787.647600.903906.710305.65890HepG2HNRNPF
SCN1AENSG00000144285.111396.61330985.577800.502804.796103.89760HepG2HNRNPK
SCN1AENSG00000144285.112002.128801113.007700.8470029.3970027.48090HepG2HNRNPL
SCN1AENSG00000144285.11582.12530966.40970-0.731309.188907.62660HepG2HNRNPM
SCN1AENSG00000144285.111628.86130775.586601.070408.983307.74880HepG2IGF2BP1
SCN1AENSG00000144285.11413.33760989.57280-1.2595019.1160017.52080HepG2IGF2BP2
SCN1AENSG00000144285.111350.434501132.030400.254402.415001.46170HepG2KIF1C
SCN1AENSG00000144285.111620.359301150.029100.494503.449902.52140HepG2LARP4
SCN1AENSG00000144285.11552.98580981.93490-0.8284010.997108.88470HepG2LARP7
SCN1AENSG00000144285.111494.867101030.943300.536005.562103.84960HepG2LIN28B
SCN1AENSG00000144285.111510.085601049.714900.524504.356003.53580HepG2MAGOH
SCN1AENSG00000144285.11382.99500819.84850-1.098008.355206.62660HepG2METAP2
SCN1AENSG00000144285.11583.207601133.68490-0.9589015.3469013.61350HepG2MSI2
SCN1AENSG00000144285.111301.34080845.855500.621403.316102.24780HepG2MTPAP
SCN1AENSG00000144285.111200.30100951.899700.334402.761701.54640HepG2NAA15
SCN1AENSG00000144285.111564.792401080.499500.534204.654503.84520HepG2NCBP2
SCN1AENSG00000144285.111400.74650887.854200.657707.846205.47740HepG2NIP7
SCN1AENSG00000144285.11918.202801211.47080-0.399903.810402.91470HepG2NOL12
SCN1AENSG00000144285.11991.22320735.316900.430703.134002.33830HepG2NSUN2
SCN1AENSG00000144285.11844.633001301.67120-0.624006.927904.53140HepG2NUP35
SCN1AENSG00000144285.11240.48410665.45550-1.468404.368703.23790HepG2PABPC1
SCN1AENSG00000144285.11691.41100962.34550-0.477003.406802.61080HepG2PABPC4
SCN1AENSG00000144285.11565.15010719.08430-0.347502.965402.09150HepG2PARN
SCN1AENSG00000144285.111570.27770982.074000.6770014.6633013.44590HepG2PCBP1
SCN1AENSG00000144285.111574.394801177.654700.418803.510001.55670HepG2PES1
SCN1AENSG00000144285.11920.24780647.955600.506006.087705.02680HepG2PPIL4
SCN1AENSG00000144285.112161.447801281.875400.753608.154406.91960HepG2PRPF4
SCN1AENSG00000144285.113371.319901185.279401.5080021.7652018.97330HepG2PRPF6
SCN1AENSG00000144285.11944.05230616.245600.615305.617104.50880HepG2PRPF8
SCN1AENSG00000144285.111869.01200999.254300.9033025.8313024.48480HepG2PTBP1
SCN1AENSG00000144285.11941.059901227.45250-0.383303.933703.25350HepG2PUM1
SCN1AENSG00000144285.11369.027801226.61310-1.7329032.4342030.32090HepG2PUM2
SCN1AENSG00000144285.113068.111401261.257901.2824072.4730070.25170HepG2PUS1
SCN1AENSG00000144285.112645.147001082.308001.2891044.6150042.67510HepG2QKI
SCN1AENSG00000144285.11284.904001088.19570-1.9334016.4308014.85690HepG2RAVER1
SCN1AENSG00000144285.11555.763302219.58250-1.9977054.6639052.93520HepG2RBM22
SCN1AENSG00000144285.112430.41420982.229701.3070037.7179035.48490HepG2RBM25
SCN1AENSG00000144285.11280.13350703.19750-1.327803.713801.94250HepG2RBM47
SCN1AENSG00000144285.111311.86770961.513200.448103.087401.96630HepG2RCC2
SCN1AENSG00000144285.111827.265001112.109600.7163011.8098010.84190HepG2NELFE
SCN1AENSG00000144285.112372.534701035.714601.1957048.7656046.83630HepG2RECQL
SCN1AENSG00000144285.11493.25080848.81110-0.783103.192802.46660HepG2RPLP0
SCN1AENSG00000144285.112875.594201068.593501.4280019.5328017.28180HepG2RPS10
SCN1AENSG00000144285.11548.18800762.21430-0.475503.962203.23930HepG2RPS19
SCN1AENSG00000144285.111166.03790730.535500.674503.584902.67310HepG2RPS3A
SCN1AENSG00000144285.11789.899901114.71720-0.496904.380703.01300HepG2RPS5
SCN1AENSG00000144285.111524.23140646.956301.2362047.0948044.94270HepG2SAFB2
SCN1AENSG00000144285.111416.26130694.476501.028003.558601.79420HepG2SBDS
SCN1AENSG00000144285.11381.58770765.01940-1.0035012.1495010.25320HepG2SERBP1
SCN1AENSG00000144285.111511.844902101.27680-0.475002.494501.85500HepG2SF3A3
SCN1AENSG00000144285.111764.342001108.595700.6703013.8758012.51240HepG2SLBP
SCN1AENSG00000144285.11633.561001108.52930-0.807105.450604.07420HepG2SMNDC1
SCN1AENSG00000144285.111773.890101058.038500.745406.655004.14110HepG2SND1
SCN1AENSG00000144285.112007.253902506.91480-0.320705.260504.63040HepG2SRFBP1
SCN1AENSG00000144285.112451.592201085.951601.1747013.6928012.81280HepG2SRSF1
SCN1AENSG00000144285.111335.38630773.912000.786906.191905.21700HepG2SRSF7
SCN1AENSG00000144285.111153.17900883.452600.384304.826804.13570HepG2SRSF9
SCN1AENSG00000144285.114244.073302176.557400.9633046.9825045.50040HepG2SSB
SCN1AENSG00000144285.11878.374301298.45690-0.563906.941206.03440HepG2SUCLG1
SCN1AENSG00000144285.11417.29750945.86720-1.1806020.7833018.45560HepG2SUPT6H
SCN1AENSG00000144285.11205.82380795.09620-1.9497030.4408028.64880HepG2SUPV3L1
SCN1AENSG00000144285.113156.67430976.009001.6933079.5423077.07450HepG2TAF15
SCN1AENSG00000144285.112850.20680808.424601.8178059.6678057.13760HepG2TARDBP
SCN1AENSG00000144285.11286.18830532.95040-0.897007.096405.62520HepG2TFIP11
SCN1AENSG00000144285.111789.555601092.354800.712105.577703.53100HepG2TRA2A
SCN1AENSG00000144285.111498.714501129.580400.407803.771602.73690HepG2TUFM
SCN1AENSG00000144285.11816.712101572.84000-0.945502.883501.87350HepG2U2AF2
SCN1AENSG00000144285.11233.39570469.71620-1.009009.172307.79080HepG2UCHL5
SCN1AENSG00000144285.11516.166501863.51510-1.8521098.5391095.73350HepG2UPF1
SCN1AENSG00000144285.111140.126101915.40390-0.7485018.3939016.10540HepG2UTP18
SCN1AENSG00000144285.111394.196001799.14470-0.367904.785304.03300HepG2UTP3
SCN1AENSG00000144285.111298.03720782.683800.729708.337907.09330HepG2XRN2
SCN1AENSG00000144285.111526.329601265.081000.270703.361902.63230HepG2ZC3H8
SCN1AENSG00000144285.11664.605702049.50440-1.6247092.9680091.00720HepG2ZNF622
SCN1AENSG00000144285.111929.632401086.862200.828108.161705.83900HepG2ZRANB2
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 SCN1A is not available on ENCORE database.





4 RBPs can affect the splicing of SCN1A :

Event TypeGene NameGene IDchrStrandExonStartExonEnd2ndExonStart2ndExonEndupstreamESupstreamEEdownstreamESdownstreamEEdPSIp-valueFDRis_includedCell LineAffected by RBPBound by RBP
SESCN1AENSG00000144285.11chr2-166858981166859263166856232166856286166866228166866351-0.571000.000550.01562excludedHepG2SRSF1
SESCN1AENSG00000144285.11chr2-1668637391668638031668589811668592631668662281668663510.433000.000870.04174includedHepG2SF3B4
SESCN1AENSG00000144285.11chr2-1668637391668638031668589811668592631668662281668663510.455000.000110.01793includedHepG2TAF15
MXESCN1AENSG00000144285.11chr2-1668589811668592631668637391668638031668562321668562861668662281668663510.579000.000140.004531includedHepG2SRSF1
MXESCN1AENSG00000144285.11chr2-1668589811668591141668637391668638031668562321668562861668662281668663510.513000.002040.046091includedHepG2HNRNPK

*: "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 SCN1A is not avaliable on ENCORE database.