U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SNTA1 syntrophin alpha 1 [ Homo sapiens (human) ]

Gene ID: 6640, updated on 19-Sep-2024

Summary

Official Symbol
SNTA1provided by HGNC
Official Full Name
syntrophin alpha 1provided by HGNC
Primary source
HGNC:HGNC:11167
See related
Ensembl:ENSG00000101400 MIM:601017; AllianceGenome:HGNC:11167
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SNT1; LQT12; TACIP1; dJ1187J4.5
Summary
Syntrophins are cytoplasmic peripheral membrane scaffold proteins that are components of the dystrophin-associated protein complex. This gene is a member of the syntrophin gene family and encodes the most common syntrophin isoform found in cardiac tissues. The N-terminal PDZ domain of this syntrophin protein interacts with the C-terminus of the pore-forming alpha subunit (SCN5A) of the cardiac sodium channel Nav1.5. This protein also associates cardiac sodium channels with the nitric oxide synthase-PMCA4b (plasma membrane Ca-ATPase subtype 4b) complex in cardiomyocytes. This gene is a susceptibility locus for Long-QT syndrome (LQT) - an inherited disorder associated with sudden cardiac death from arrhythmia - and sudden infant death syndrome (SIDS). This protein also associates with dystrophin and dystrophin-related proteins at the neuromuscular junction and alters intracellular calcium ion levels in muscle tissue. [provided by RefSeq, Jan 2013]
Expression
Broad expression in heart (RPKM 50.7), thyroid (RPKM 41.8) and 19 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SNTA1 in Genome Data Viewer
Location:
20q11.21
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (33407957..33443763, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (35135186..35170977, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (31995763..32031569, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31934530-31935364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31937032-31937864 Neighboring gene BPI fold containing family B member 9, pseudogene Neighboring gene CDK5 regulatory subunit associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17730 Neighboring gene uncharacterized LOC124904889 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32006871-32007371 Neighboring gene VISTA enhancer hs2173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17731 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:32027926-32028104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32032043-32032543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32064897-32065812 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32077069-32077617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12814 Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32104950-32105714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32115920-32116420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32116421-32116921 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32118677-32119177 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32121705-32122204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32124101-32124819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32144891-32145546 Neighboring gene Sharpr-MPRA regulatory region 10659 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32156001-32156927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32169053-32169552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32169790-32170374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32170375-32170958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32175233-32175732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32240942-32241530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32244101-32244601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32250716-32251654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32251655-32252591 Neighboring gene chromosome 20 open reading frame 144 Neighboring gene N-terminal EF-hand calcium binding protein 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Yeast two hybrid assay identifies the HIV-1 Nef-interacting protein syntrophin PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables PDZ domain binding IEA
Inferred from Electronic Annotation
more info
 
enables actin binding IEA
Inferred from Electronic Annotation
more info
 
enables calmodulin binding IEA
Inferred from Electronic Annotation
more info
 
enables nitric-oxide synthase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sodium channel regulator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables structural molecule activity IEA
Inferred from Electronic Annotation
more info
 
enables transmembrane transporter binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
part_of dystrophin-associated glycoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in intracellular anatomical structure IBA
Inferred from Biological aspect of Ancestor
more info
 
colocalizes_with lateral plasma membrane TAS
Traceable Author Statement
more info
PubMed 
is_active_in neuromuscular junction IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in sarcolemma IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of syntrophin complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
alpha-1-syntrophin
Names
59 kDa dystrophin-associated protein A1 acidic component 1
acidic alpha 1 syntrophin
dystrophin-associated protein A1, 59kDa, acidic component
pro-TGF-alpha cytoplasmic domain-interacting protein 1
syntrophin-1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011622.1 RefSeqGene

    Range
    5001..40936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_332

mRNA and Protein(s)

  1. NM_001424413.1NP_001411342.1  alpha-1-syntrophin isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL355392
  2. NM_001424414.1NP_001411343.1  alpha-1-syntrophin isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL355392
  3. NM_003098.3NP_003089.1  alpha-1-syntrophin isoform 1

    See identical proteins and their annotated locations for NP_003089.1

    Status: REVIEWED

    Source sequence(s)
    AL355392
    Consensus CDS
    CCDS13220.1
    UniProtKB/Swiss-Prot
    A8K7H9, B4DX40, E1P5N1, Q13424, Q16438
    Related
    ENSP00000217381.2, ENST00000217381.3
    Conserved Domains (4) summary
    smart00233
    Location:298401
    PH; Pleckstrin homology domain
    cd00992
    Location:86167
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd01258
    Location:209270
    PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain
    pfam00169
    Location:298401
    PH; PH domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    33407957..33443763 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529008.2XP_011527310.1  alpha-1-syntrophin isoform X3

    Conserved Domains (4) summary
    smart00233
    Location:298401
    PH; Pleckstrin homology domain
    cd00992
    Location:86167
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd01258
    Location:209270
    PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain
    pfam00169
    Location:298401
    PH; PH domain
  2. XM_047440392.1XP_047296348.1  alpha-1-syntrophin isoform X4

  3. XM_024451971.2XP_024307739.1  alpha-1-syntrophin isoform X5

    UniProtKB/TrEMBL
    B3KTR0
    Conserved Domains (3) summary
    cd00992
    Location:158
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd01258
    Location:100161
    PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain
    pfam00169
    Location:189292
    PH; PH domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    35135186..35170977 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323891.1XP_054179866.1  alpha-1-syntrophin isoform X3

  2. XM_054323892.1XP_054179867.1  alpha-1-syntrophin isoform X4

  3. XM_054323893.1XP_054179868.1  alpha-1-syntrophin isoform X5

    UniProtKB/TrEMBL
    B3KTR0