Tissue expression of SCN1A - Summary - The Human Protein Atlas

GENERAL INFORMATION
Gene name	SCN1A
Gene description	Sodium channel, voltage gated, type I alpha subunit
Protein class	Disease related genes FDA approved drug targets Predicted membrane proteins Transporters Voltage-gated ion channels
Predicted localization	Membrane
Number of transcripts	4
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HUMAN PROTEIN ATLAS INFORMATION

RNA tissue category

HPA:	Tissue enhanced (cerebral cortex, fallopian tube, lung)
GTEx:	Group enriched (caudate, cerebellum, cerebral cortex, hippocampus, hypothalamus, lung)
FANTOM5:	Group enriched (brain, caudate, cerebellum, hippocampus)

Protein evidence

Evidence at protein level

DATA RELIABILITY
Reliability score	Pending normal tissue annotation.

RNA AND PROTEIN EXPRESSION SUMMARY

RNA expression (TPM)

Protein expression (score)

Brain

N/A

Cerebral cortex

N/A

Hippocampus

N/A

Caudate

N/A

Cerebellum

N/A

Endocrine tissues

N/A

Thyroid gland

N/A

Parathyroid gland

N/A

Adrenal gland

N/A

Bone marrow & immune system

N/A

Appendix

N/A

Bone marrow

N/A

Lymph node

N/A

Tonsil

N/A

Spleen

N/A

Muscle tissues

N/A

Heart muscle

N/A

Skeletal muscle

N/A

Smooth muscle

N/A

Lung

N/A

Nasopharynx

N/A

Bronchus

N/A

Lung

N/A

Liver & gallbladder

N/A

Liver

N/A

Gallbladder

N/A

Pancreas

N/A

Pancreas

N/A

Gastrointestinal tract

N/A

Oral mucosa

N/A

Salivary gland

N/A

Esophagus

N/A

Stomach

N/A

Duodenum

N/A

Small intestine

N/A

Colon

N/A

Rectum

N/A

Kidney & urinary bladder

N/A

Kidney

N/A

Urinary bladder

N/A

Male tissues

N/A

Testis

N/A

Epididymis

N/A

Prostate

N/A

Seminal vesicle

N/A

Female tissues

N/A

Breast

N/A

Vagina

N/A

Cervix, uterine

N/A

Endometrium

N/A

Fallopian tube

N/A

Ovary

N/A

Placenta

N/A

Adipose & soft tissue

N/A

Adipose tissue

N/A

Soft tissue

N/A

Skin

N/A

Skin

N/A

PROTEIN EXPRESSION OVERVIEW
Pending normal tissue annotation.

RNA EXPRESSION OVERVIEW
HPA dataset Organ Expression Alphabetical RNA tissue category: Tissue enhanced (cerebral cortex, fallopian tube, lung)
GTEx dataset Organ Expression Alphabetical RNA tissue category: Group enriched (caudate, cerebellum, cerebral cortex, hippocampus, hypothalamus, lung)
FANTOM5 dataset Organ Expression Alphabetical RNA tissue category: Group enriched (brain, caudate, cerebellum, hippocampus)

GENE INFORMATION
Gene name	SCN1A (HGNC Symbol)
Synonyms	FEB3, GEFSP2, HBSCI, NAC1, Nav1.1, SCN1, SMEI
Description	Sodium channel, voltage gated, type I alpha subunit (HGNC Symbol)
Entrez gene summary	Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015]
Chromosome	2
Cytoband	q24.3
Chromosome location (bp)	165989160 - 166128047
Protein evidence	Evidence at protein level (all genes)
Ensembl	ENSG00000144285 (version 83.38)
Entrez gene	6323
UniProt	P35498 (UniProt - Evidence at protein level)
neXtProt	NX_P35498
Antibodypedia	SCN1A antibodies

PROTEIN BROWSER

SCN1A-001	SCN1A-002	SCN1A-003	SCN1A-201

PROTEIN INFORMATION
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
SCN1A-001 ENSP00000303540 ENST00000303395	P35498 [Direct mapping] Sodium channel protein type 1 subunit alpha Show all	Transporters Transporter channels and pores Voltage-gated ion channels Voltage-Gated Sodium Channels Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Show all	GO:0001508 [action potential] GO:0001518 [voltage-gated sodium channel complex] GO:0002230 [positive regulation of defense response to virus by host] GO:0005216 [ion channel activity] GO:0005248 [voltage-gated sodium channel activity] GO:0005886 [plasma membrane] GO:0006811 [ion transport] GO:0006814 [sodium ion transport] GO:0007628 [adult walking behavior] GO:0014704 [intercalated disc] GO:0016020 [membrane] GO:0019227 [neuronal action potential propagation] GO:0019228 [neuronal action potential] GO:0030018 [Z disc] GO:0030315 [T-tubule] GO:0030424 [axon] GO:0031402 [sodium ion binding] GO:0033268 [node of Ranvier] GO:0034706 [sodium channel complex] GO:0034765 [regulation of ion transmembrane transport] GO:0035725 [sodium ion transmembrane transport] GO:0042391 [regulation of membrane potential] GO:0043025 [neuronal cell body] GO:0043194 [axon initial segment] GO:0050884 [neuromuscular process controlling posture] GO:0055085 [transmembrane transport] GO:0086010 [membrane depolarization during action potential] Show all	2009 aa 229 kDa	No	>9
SCN1A-002 ENSP00000364554 ENST00000375405	P35498 [Direct mapping] Sodium channel protein type 1 subunit alpha Show all	Transporters Transporter channels and pores Voltage-gated ion channels Voltage-Gated Sodium Channels Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Show all	GO:0001518 [voltage-gated sodium channel complex] GO:0002230 [positive regulation of defense response to virus by host] GO:0005216 [ion channel activity] GO:0005248 [voltage-gated sodium channel activity] GO:0005886 [plasma membrane] GO:0006811 [ion transport] GO:0006814 [sodium ion transport] GO:0016020 [membrane] GO:0019228 [neuronal action potential] GO:0030018 [Z disc] GO:0034765 [regulation of ion transmembrane transport] GO:0035725 [sodium ion transmembrane transport] GO:0055085 [transmembrane transport] GO:0086010 [membrane depolarization during action potential] Show all	1998 aa 227.8 kDa	No	>9
SCN1A-003 ENSP00000386312 ENST00000409050	P35498 [Direct mapping] Sodium channel protein type 1 subunit alpha Show all	Transporters Transporter channels and pores Voltage-gated ion channels Voltage-Gated Sodium Channels Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Show all	GO:0001518 [voltage-gated sodium channel complex] GO:0002230 [positive regulation of defense response to virus by host] GO:0005216 [ion channel activity] GO:0005248 [voltage-gated sodium channel activity] GO:0005886 [plasma membrane] GO:0006811 [ion transport] GO:0006814 [sodium ion transport] GO:0016020 [membrane] GO:0019228 [neuronal action potential] GO:0030018 [Z disc] GO:0034765 [regulation of ion transmembrane transport] GO:0035725 [sodium ion transmembrane transport] GO:0055085 [transmembrane transport] GO:0086010 [membrane depolarization during action potential] Show all	1981 aa 226.2 kDa	No	>9
SCN1A-201 ENSP00000407030 ENST00000423058	P35498 [Direct mapping] Sodium channel protein type 1 subunit alpha Show all	Transporters Transporter channels and pores Voltage-gated ion channels Voltage-Gated Sodium Channels Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes FDA approved drug targets Small molecule drugs Show all	GO:0001518 [voltage-gated sodium channel complex] GO:0002230 [positive regulation of defense response to virus by host] GO:0005216 [ion channel activity] GO:0005248 [voltage-gated sodium channel activity] GO:0005886 [plasma membrane] GO:0006811 [ion transport] GO:0006814 [sodium ion transport] GO:0016020 [membrane] GO:0019228 [neuronal action potential] GO:0030018 [Z disc] GO:0034765 [regulation of ion transmembrane transport] GO:0035725 [sodium ion transmembrane transport] GO:0055085 [transmembrane transport] GO:0086010 [membrane depolarization during action potential] Show all	2009 aa 229 kDa	No	>9