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Aliases for SMARCA1 Gene

Aliases for SMARCA1 Gene

  • SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A, Member 1 2 3 5
  • Nucleosome-Remodeling Factor Subunit SNF2L 3 4
  • ATP-Dependent Helicase SMARCA1 3 4
  • SNF2L1 3 4
  • SNF2L 3 4
  • SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily A Member 1 4
  • Global Transcription Activator Homologous Sequence 3
  • Probable Global Transcription Activator SNF2L1 3
  • Sucrose Nonfermenting 2-Like Protein 1 3
  • SNF2-Like 1 3
  • EC 3.6.4.- 4
  • NURF140 3
  • SNF2LB 3
  • SNF2LT 3
  • HSNF2L 3
  • ISWI 3
  • SWI2 3
  • SWI 3

External Ids for SMARCA1 Gene

Previous HGNC Symbols for SMARCA1 Gene

  • SNF2L1
  • SNF2L

Previous GeneCards Identifiers for SMARCA1 Gene

  • GC0XM123226
  • GC0XM125426
  • GC0XM126525
  • GC0XM127286
  • GC0XM128306
  • GC0XM128408
  • GC0XM128580
  • GC0XM117987

Summaries for SMARCA1 Gene

Entrez Gene Summary for SMARCA1 Gene

  • This gene encodes a member of the SWI/SNF family of proteins. The encoded protein is an ATPase which is expressed in diverse tissues and contributes to the chromatin remodeling complex that is involved in transcription. The protein may also play a role in DNA damage, growth inhibition and apoptosis of cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

GeneCards Summary for SMARCA1 Gene

SMARCA1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A, Member 1) is a Protein Coding gene. Diseases associated with SMARCA1 include Alpha Thalassemia-X-Linked Intellectual Disability Syndrome and Schimke Immunoosseous Dysplasia. Among its related pathways are Platinum Pathway, Pharmacokinetics/Pharmacodynamics and PEDF Induced Signaling. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and hydrolase activity. An important paralog of this gene is SMARCA5.

UniProtKB/Swiss-Prot for SMARCA1 Gene

  • Energy-transducing component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes. Both complexes facilitate the perturbation of chromatin structure in an ATP-dependent manner. Potentiates neurite outgrowth. May be involved in brain development by regulating En-1 and En-2 expression. May be involved in the development of luteal cells.

Gene Wiki entry for SMARCA1 Gene

Additional gene information for SMARCA1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMARCA1 Gene

Genomics for SMARCA1 Gene

GeneHancer (GH) Regulatory Elements for SMARCA1 Gene

Promoters and enhancers for SMARCA1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ129521 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.7 686 3.3 ARID4B SIN3A DMAP1 ZNF48 ZNF335 GLIS2 SCRT2 ZNF362 ZNF398 ZEB2 SMARCA1 ENSG00000252170 GC0XP129460
GH0XJ129789 Enhancer 0.4 dbSUPER 14.9 -267.5 -267542 3.2 SCRT1 SCRT2 ZNF112 SMARCA1 XPNPEP2 OCRL ZDHHC9 UTP14A APLN ENSG00000240143 SASH3 GC0XP129460
GH0XJ129519 Enhancer 0.9 ENCODE dbSUPER 0.7 +3.2 3237 1.2 SOX13 FOXA2 SAP130 ZSCAN4 CEBPG RARA NR2F6 CREM TEAD1 HLF ENSG00000252170 GC0XP129519 SMARCA1 GC0XP129460
GH0XJ129510 Enhancer 0.9 ENCODE dbSUPER 0.4 +12.8 12843 1.3 SOX13 SAP130 RARA TEAD3 NR2F6 GATAD2A SOX5 TEAD1 ETV5 NFIL3 GC0XP129519 SMARCA1 GC0XP129460
GH0XJ129532 Promoter 0.5 EPDnew 0.4 -9.2 -9188 0.1 OCRL SMARCA1 GC0XP129460
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMARCA1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMARCA1 gene promoter:
  • AP-2alpha isoform 3
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alphaA
  • AP-2alpha isoform 4

Genomic Locations for SMARCA1 Gene

Genomic Locations for SMARCA1 Gene
chrX:129,446,501-129,523,513
(GRCh38/hg38)
Size:
77,013 bases
Orientation:
Minus strand
chrX:128,580,478-128,657,477
(GRCh37/hg19)
Size:
77,000 bases
Orientation:
Minus strand

Genomic View for SMARCA1 Gene

Genes around SMARCA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMARCA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMARCA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMARCA1 Gene

Proteins for SMARCA1 Gene

  • Protein details for SMARCA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P28370-SMCA1_HUMAN
    Recommended name:
    Probable global transcription activator SNF2L1
    Protein Accession:
    P28370
    Secondary Accessions:
    • Q5JV41
    • Q5JV42

    Protein attributes for SMARCA1 Gene

    Size:
    1054 amino acids
    Molecular mass:
    122605 Da
    Quaternary structure:
    • Part of the nucleosome-remodeling factor (NURF) complex which consists of SMARCA1; BPTF; RBBP4 and RBBP7. Part of the CECR2-containing-remodeling factor (CERF) complex which contains CECR2 and SMARCA1. Interacts with PRLR.
    SequenceCaution:
    • Sequence=AAA80560.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SMARCA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMARCA1 Gene

Post-translational modifications for SMARCA1 Gene

  • Ubiquitination at isoforms=2851, isoforms=2662, and posLast=179179
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SMARCA1 Gene

Domains & Families for SMARCA1 Gene

Gene Families for SMARCA1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry

P28370

UniProtKB/Swiss-Prot:

SMCA1_HUMAN :
  • Belongs to the SNF2/RAD54 helicase family. ISWI subfamily.
Family:
  • Belongs to the SNF2/RAD54 helicase family. ISWI subfamily.
genes like me logo Genes that share domains with SMARCA1: view

Function for SMARCA1 Gene

Molecular function for SMARCA1 Gene

UniProtKB/Swiss-Prot Function:
Energy-transducing component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes. Both complexes facilitate the perturbation of chromatin structure in an ATP-dependent manner. Potentiates neurite outgrowth. May be involved in brain development by regulating En-1 and En-2 expression. May be involved in the development of luteal cells.
GENATLAS Biochemistry:
general transcriptional activator S cerevisiae SWI/SNF related protein,matrix associated,actin-dependent regulator of chromatin,subfamily A,member 1,component of the chromatin remodeling complex,Drosophila ISWI (initiator of SWI) homolog

Enzyme Numbers (IUBMB) for SMARCA1 Gene

Gene Ontology (GO) - Molecular Function for SMARCA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 14609955
genes like me logo Genes that share ontologies with SMARCA1: view
genes like me logo Genes that share phenotypes with SMARCA1: view

Animal Model Products

miRNA for SMARCA1 Gene

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMARCA1 Gene

Localization for SMARCA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMARCA1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMARCA1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMARCA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IEA --
GO:0005634 nucleus IDA,IEA 14609955
GO:0005654 nucleoplasm IDA --
GO:0016589 NURF complex IDA,IEA 20850016
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with SMARCA1: view

Pathways & Interactions for SMARCA1 Gene

genes like me logo Genes that share pathways with SMARCA1: view

Pathways by source for SMARCA1 Gene

1 Cell Signaling Technology pathway for SMARCA1 Gene

Gene Ontology (GO) - Biological Process for SMARCA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000733 DNA strand renaturation IEA --
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IDA,IEA 14609955
GO:0006351 transcription, DNA-templated IMP 14609955
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with SMARCA1: view

No data available for SIGNOR curated interactions for SMARCA1 Gene

Drugs & Compounds for SMARCA1 Gene

No Compound Related Data Available

Transcripts for SMARCA1 Gene

Unigene Clusters for SMARCA1 Gene

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMARCA1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23 ^
SP1:
SP2: -
SP3:
SP4:
SP5:

ExUns: 24a · 24b · 24c ^ 25a · 25b · 25c · 25d
SP1:
SP2:
SP3:
SP4: - -
SP5: -

Relevant External Links for SMARCA1 Gene

GeneLoc Exon Structure for
SMARCA1
ECgene alternative splicing isoforms for
SMARCA1

Expression for SMARCA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMARCA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMARCA1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.9), Tlymphocyte (11.4), and Fetal gut (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMARCA1 Gene



Protein tissue co-expression partners for SMARCA1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMARCA1 Gene:

SMARCA1

SOURCE GeneReport for Unigene cluster for SMARCA1 Gene:

Hs.152292

Evidence on tissue expression from TISSUES for SMARCA1 Gene

  • Liver(4.4)
  • Kidney(4.3)
  • Lung(4.3)
  • Nervous system(2.6)
genes like me logo Genes that share expression patterns with SMARCA1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMARCA1 Gene

Orthologs for SMARCA1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SMARCA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMARCA1 33
  • 96.84 (n)
dog
(Canis familiaris)
Mammalia SMARCA1 34 33
  • 94.29 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMARCA1 34 33
  • 93.38 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarca1 33
  • 91.9 (n)
mouse
(Mus musculus)
Mammalia Smarca1 16 34 33
  • 91.78 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMARCA1 34
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMARCA1 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMARCA1 34 33
  • 82.18 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMARCA1 34
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smarca1 33
  • 78.84 (n)
zebrafish
(Danio rerio)
Actinopterygii smarca1 34
  • 82 (a)
OneToOne
LOC559803 33
  • 74.88 (n)
Dr.12723 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13579 33
fruit fly
(Drosophila melanogaster)
Insecta Iswi 34 35 33
  • 65.37 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010700 33
  • 64.75 (n)
worm
(Caenorhabditis elegans)
Secernentea isw-1 34 33
  • 62.38 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ISW2 34 33
  • 57.27 (n)
OneToMany
ISW1 36
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F24838g 33
  • 56.1 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR537W 33
  • 55.18 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.4483 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6886 34
  • 70 (a)
OneToMany
Species where no ortholog for SMARCA1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMARCA1 Gene

ENSEMBL:
Gene Tree for SMARCA1 (if available)
TreeFam:
Gene Tree for SMARCA1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMARCA1: view image

Paralogs for SMARCA1 Gene

Paralogs for SMARCA1 Gene

(15) SIMAP similar genes for SMARCA1 Gene using alignment to 3 proteins:

  • SMCA1_HUMAN
  • B7ZLQ5_HUMAN
  • Q86UA8_HUMAN
genes like me logo Genes that share paralogs with SMARCA1: view

Variants for SMARCA1 Gene

Sequence variations from dbSNP and Humsavar for SMARCA1 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1060499736 likely-pathogenic, Abnormality of brain morphology 129,523,364(-) G/A coding_sequence_variant, stop_gained
rs140388140 likely-benign, not specified 129,487,119(-) G/A coding_sequence_variant, missense_variant
rs1000034792 -- 129,446,045(-) G/A downstream_transcript_variant
rs1000100117 -- 129,494,441(-) T/C intron_variant
rs1000107171 -- 129,510,254(-) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SMARCA1 Gene

Variant ID Type Subtype PubMed ID
nsv525860 CNV gain 19592680
nsv523064 CNV gain 19592680
esv3574553 CNV loss 25503493
esv3574551 CNV loss 25503493

Variation tolerance for SMARCA1 Gene

Residual Variation Intolerance Score: 8.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.30; 41.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMARCA1 Gene

Human Gene Mutation Database (HGMD)
SMARCA1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMARCA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMARCA1 Gene

Disorders for SMARCA1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SMARCA1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
alpha thalassemia-x-linked intellectual disability syndrome
  • alpha-thalassemia/mental retardation syndrome nondeletion type
schimke immunoosseous dysplasia
  • siod
charge syndrome
  • charge association--coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SMARCA1

genes like me logo Genes that share disorders with SMARCA1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMARCA1 Gene

Publications for SMARCA1 Gene

  1. Isolation of human NURF: a regulator of Engrailed gene expression. (PMID: 14609955) Barak O … Shiekhattar R (The EMBO journal 2003) 2 3 4 58
  2. Cloning of human and bovine homologs of SNF2/SWI2: a global activator of transcription in yeast S. cerevisiae. (PMID: 1408766) Okabe I … Nussbaum RL (Nucleic acids research 1992) 2 3 4 58
  3. Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26. (PMID: 18302774) Lazzaro MA … Picketts DJ (BMC medical genetics 2008) 3 22 58
  4. The imitation switch protein SNF2L regulates steroidogenic acute regulatory protein expression during terminal differentiation of ovarian granulosa cells. (PMID: 16740656) Lazzaro MA … Picketts DJ (Molecular endocrinology (Baltimore, Md.) 2006) 3 4 58
  5. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. (PMID: 16728976) Wysocka J … Allis CD (Nature 2006) 3 22 58

Products for SMARCA1 Gene

Sources for SMARCA1 Gene

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