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Aliases for SMARCD1 Gene

Aliases for SMARCD1 Gene

  • SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily D, Member 1 2 3 5
  • 60 KDa BRG-1/Brm-Associated Factor Subunit A 3 4
  • BRG1-Associated Factor 60A 3 4
  • BAF60A 3 4
  • Mammalian Chromatin Remodeling Complex BRG1-Associated Factor 60A 3
  • Chromatin Remodeling Complex BAF60A Subunit 3
  • SWI/SNF Complex 60 KDa Subunit A 3
  • SWI/SNF Complex 60 KDa Subunit 4
  • Swp73-Like Protein 3
  • CRACD1 3
  • Rsc6p 3

External Ids for SMARCD1 Gene

Previous GeneCards Identifiers for SMARCD1 Gene

  • GC12P050773
  • GC12P050535
  • GC12P050195
  • GC12P048766
  • GC12P048767
  • GC12P048768
  • GC12P050478
  • GC12P047511

Summaries for SMARCD1 Gene

Entrez Gene Summary for SMARCD1 Gene

  • The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SMARCD1 Gene

SMARCD1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily D, Member 1) is a Protein Coding gene. Among its related pathways are Prostate Cancer and AMPK Enzyme Complex Pathway. GO annotations related to this gene include transcription coactivator activity and protein complex scaffold. An important paralog of this gene is SMARCD2.

UniProtKB/Swiss-Prot for SMARCD1 Gene

  • Involved in chromatin remodeling. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Has a strong influence on vitamin D-mediated transcriptional activity from an enhancer vitamin D receptor element (VDRE). May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor (VDR) heterodimer. Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation.

Gene Wiki entry for SMARCD1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMARCD1 Gene

Genomics for SMARCD1 Gene

Regulatory Elements for SMARCD1 Gene

Promoters for SMARCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SMARCD1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SMARCD1 Gene

Chromosome:
12
Start:
50,084,972 bp from pter
End:
50,100,712 bp from pter
Size:
15,741 bases
Orientation:
Plus strand

Genomic View for SMARCD1 Gene

Genes around SMARCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMARCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMARCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMARCD1 Gene

Proteins for SMARCD1 Gene

  • Protein details for SMARCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96GM5-SMRD1_HUMAN
    Recommended name:
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
    Protein Accession:
    Q96GM5
    Secondary Accessions:
    • A6NN27
    • Q92924
    • Q9Y635

    Protein attributes for SMARCD1 Gene

    Size:
    515 amino acids
    Molecular mass:
    58233 Da
    Quaternary structure:
    • Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Specifically interacts with the VDR heterodimer complex. Interacts with ESR1, NR3C1, NR1H4, PGR, SMARCA4, SMARCC1 and SMARCC2. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin (By similarity).
    SequenceCaution:
    • Sequence=AAC50695.1; Type=Frameshift; Positions=30; Evidence={ECO:0000305}; Sequence=AAD23390.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH09368.3; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SMARCD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMARCD1 Gene

Proteomics data for SMARCD1 Gene at MOPED

Post-translational modifications for SMARCD1 Gene

  • Ubiquitination at Lys 101, Lys 223, and Lys 464
  • Modification sites at PhosphoSitePlus

Other Protein References for SMARCD1 Gene

Antibody Products

No data available for DME Specific Peptides for SMARCD1 Gene

Domains & Families for SMARCD1 Gene

Protein Domains for SMARCD1 Gene

Suggested Antigen Peptide Sequences for SMARCD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96GM5

UniProtKB/Swiss-Prot:

SMRD1_HUMAN :
  • Contains 1 SWIB domain.
  • Belongs to the SMARCD family.
Domain:
  • Contains 1 SWIB domain.
Family:
  • Belongs to the SMARCD family.
genes like me logo Genes that share domains with SMARCD1: view

No data available for Gene Families for SMARCD1 Gene

Function for SMARCD1 Gene

Molecular function for SMARCD1 Gene

GENATLAS Biochemistry:
general transcriptional activator S cerevisiae SWI/SNF related protein,matrix associated,actin-dependent regulator of chromatin,subfamily D,member 1,component of the chromatin remodeling complex,ubiquitously expressed
UniProtKB/Swiss-Prot Function:
Involved in chromatin remodeling. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Has a strong influence on vitamin D-mediated transcriptional activity from an enhancer vitamin D receptor element (VDRE). May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor (VDR) heterodimer. Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation.

Gene Ontology (GO) - Molecular Function for SMARCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding IEA --
genes like me logo Genes that share ontologies with SMARCD1: view
genes like me logo Genes that share phenotypes with SMARCD1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMARCD1 Gene

Localization for SMARCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMARCD1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMARCD1 Gene COMPARTMENTS Subcellular localization image for SMARCD1 gene
Compartment Confidence
nucleus 5
cytosol 2
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SMARCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0071564 npBAF complex ISS --
genes like me logo Genes that share ontologies with SMARCD1: view

Pathways & Interactions for SMARCD1 Gene

genes like me logo Genes that share pathways with SMARCD1: view

Gene Ontology (GO) - Biological Process for SMARCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IEA --
GO:0071398 cellular response to fatty acid IEA --
genes like me logo Genes that share ontologies with SMARCD1: view

No data available for SIGNOR curated interactions for SMARCD1 Gene

Drugs & Compounds for SMARCD1 Gene

No Compound Related Data Available

Transcripts for SMARCD1 Gene

Unigene Clusters for SMARCD1 Gene

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

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMARCD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b · 14c · 14d
SP1: - - - -
SP2: - - - - -
SP3: - - - -
SP4: - -
SP5:
SP6: -
SP7:
SP8:

Relevant External Links for SMARCD1 Gene

GeneLoc Exon Structure for
SMARCD1
ECgene alternative splicing isoforms for
SMARCD1

Expression for SMARCD1 Gene

mRNA expression in normal human tissues for SMARCD1 Gene

Protein differential expression in normal tissues from HIPED for SMARCD1 Gene

This gene is overexpressed in Heart (31.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SMARCD1 Gene



SOURCE GeneReport for Unigene cluster for SMARCD1 Gene Hs.79335

mRNA Expression by UniProt/SwissProt for SMARCD1 Gene

Q96GM5-SMRD1_HUMAN
Tissue specificity: Expressed in all tissues tested, including brain, heart, kidney, liver, lung, muscle, pancreas and placenta.
genes like me logo Genes that share expression patterns with SMARCD1: view

Protein tissue co-expression partners for SMARCD1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for SMARCD1 Gene

Orthologs for SMARCD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SMARCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMARCD1 35
  • 100 (n)
  • 100 (a)
SMARCD1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMARCD1 36
  • 100 (a)
OneToOne
SMARCD1 35
  • 94.37 (n)
  • 98.83 (a)
dog
(Canis familiaris)
Mammalia SMARCD1 35
  • 95.59 (n)
  • 99.37 (a)
SMARCD1 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smarcd1 16
Smarcd1 35
  • 93.2 (n)
  • 99.42 (a)
Smarcd1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarcd1 35
  • 93.27 (n)
  • 99.81 (a)
chicken
(Gallus gallus)
Aves SMARCD1 36
  • 95 (a)
OneToOne
SMARCD1 35
  • 81.71 (n)
  • 94.34 (a)
lizard
(Anolis carolinensis)
Reptilia SMARCD1 36
  • 96 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.5492 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7704 35
smarcd1 35
  • 78.54 (n)
  • 94.09 (a)
zebrafish
(Danio rerio)
Actinopterygii smarcd1 36
  • 88 (a)
OneToOne
smarcd1 35
  • 78.51 (n)
  • 93.62 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005336 35
  • 66.74 (n)
  • 74.94 (a)
fruit fly
(Drosophila melanogaster)
Insecta Bap60 36
  • 63 (a)
OneToMany
Bap60 35
  • 64.46 (n)
  • 71.58 (a)
Bap60 37
  • 78 (a)
worm
(Caenorhabditis elegans)
Secernentea swsn-2.2 36
  • 49 (a)
ManyToMany
ham-3 36
  • 54 (a)
ManyToMany
swsn-2.1 35
  • 56.55 (n)
  • 58.42 (a)
ZK1128.5 37
  • 53 (a)
C18E3.2 37
  • 53 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G01890 35
  • 48.78 (n)
  • 38.48 (a)
rice
(Oryza sativa)
Liliopsida Os04g0382100 35
  • 50.42 (n)
  • 39.62 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4313 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 50 (a)
ManyToMany
-- 36
  • 74 (a)
ManyToMany
Species with no ortholog for SMARCD1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMARCD1 Gene

ENSEMBL:
Gene Tree for SMARCD1 (if available)
TreeFam:
Gene Tree for SMARCD1 (if available)

Paralogs for SMARCD1 Gene

Paralogs for SMARCD1 Gene

(2) SIMAP similar genes for SMARCD1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with SMARCD1: view

Variants for SMARCD1 Gene

Sequence variations from dbSNP and Humsavar for SMARCD1 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs860698 -- 50,092,539(+) TTTTT(C/T)CTTTT intron-variant
rs1063527 -- 50,089,922(+) GGCTT(C/T)CAGGT nc-transcript-variant, reference, synonymous-codon, utr-variant-3-prime
rs2307082 -- 50,086,152(+) TCTCC(C/T)CTCTG intron-variant
rs2307083 -- 50,086,770(+) CTGGT(A/G)CCAGA nc-transcript-variant, reference, synonymous-codon
rs2640533 -- 50,084,366(+) ATATT(A/T)AAAAA upstream-variant-2KB

Variation tolerance for SMARCD1 Gene

Residual Variation Intolerance Score: 18.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.68; 14.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMARCD1 Gene

HapMap Linkage Disequilibrium report
SMARCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SMARCD1 Gene

Disorders for SMARCD1 Gene

Relevant External Links for SMARCD1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMARCD1

No disorders were found for SMARCD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMARCD1 Gene

Publications for SMARCD1 Gene

  1. BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. (PMID: 12917342) Hsiao P.W. … Archer T.K. (Mol. Cell. Biol. 2003) 2 3 4 23 67
  2. Five SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) genes are dispersed in the human genome. (PMID: 9693044) Ring H.Z. … Francke U. (Genomics 1998) 2 3
  3. Diversity and specialization of mammalian SWI/SNF complexes. (PMID: 8804307) Wang W. … Crabtree G.R. (Genes Dev. 1996) 2 3
  4. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A. … Stelzl U. (Mol. Syst. Biol. 2015) 3
  5. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3

Products for SMARCD1 Gene

Sources for SMARCD1 Gene

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