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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
  • SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily D Member 1 3
  • 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 Chromatin organization and Glucocorticoid receptor regulatory network. GO annotations related to this gene include transcription coactivator activity and protein complex scaffold. An important paralog of this gene is SMARCD3.

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

Additional gene information for SMARCD1 Gene

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

Genomics for SMARCD1 Gene

Regulatory Elements for SMARCD1 Gene

Enhancers for SMARCD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H049129 1.5 ENCODE dbSUPER 92.2 -953.6 -953606 4.6 MLX FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 SP3 DDX23 SMARCD1 LMBR1L LOC390314 KMT2D BCDIN3D PRPF40B KANSL2 CCNT1 LOC100422296
GH12H051019 1.7 Ensembl ENCODE dbSUPER 63.7 +939.6 939593 11.1 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZFP41 ZNF610 SMARCD1 HNRNPA3P10 ATF1 LIMA1 LETMD1 SLC11A2 TFCP2 CSRNP2 ENSG00000257298 FAM186A
GH12H049263 1.4 ENCODE dbSUPER 58.3 -818.4 -818444 6.6 DMAP1 YY1 ZNF143 SP3 NFYC ZFP41 MEF2D GLIS1 NBN NR2C1 DDX23 CCNT1 KMT2D LMBR1L KANSL2 LOC390314 SMARCD1 BCDIN3D ENSG00000257298 ENSG00000257964
GH12H050399 1.2 ENCODE 59.5 +316.9 316911 4 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 ZNF610 ZNF585B NBN NR2C1 LIMA1 SMARCD1 PRPF40B BCDIN3D ATF1 LOC100422296 ENSG00000257298 ENSG00000257964 TFCP2 CERS5
GH12H050056 1.3 ENCODE dbSUPER 54.4 -27.5 -27502 1.1 ZNF493 ZNF133 ARID4B SIN3A GLI4 ZNF2 GLIS2 ZNF302 ZNF416 ZNF207 KMT2D SMARCD1 LMBR1L LIMA1 ATF1 BCDIN3D LOC101927267 LOC100422296 PRPF40B CERS5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMARCD1 on UCSC Golden Path with GeneCards custom track

Promoters for SMARCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000051722 328 1401 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 DEK

Genomic Locations for SMARCD1 Gene

Genomic Locations for SMARCD1 Gene
chr12:50,084,972-50,100,712
(GRCh38/hg38)
Size:
15,741 bases
Orientation:
Plus strand
chr12:50,478,755-50,494,495
(GRCh37/hg19)

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

Post-translational modifications for SMARCD1 Gene

  • Ubiquitination at Lys101, Lys223, and isoforms=464
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SMARCD1 Gene

Domains & Families for SMARCD1 Gene

Gene Families for SMARCD1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

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 :
  • Belongs to the SMARCD family.
Family:
  • Belongs to the SMARCD family.
genes like me logo Genes that share domains with SMARCD1: view

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.

Phenotypes From GWAS Catalog for SMARCD1 Gene

Gene Ontology (GO) - Molecular Function for SMARCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0003713 transcription coactivator activity NAS 8804307
GO:0005102 receptor binding IEA --
GO:0005515 protein binding IPI 12917342
GO:0032947 protein complex scaffold IDA 12917342
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

Clone 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
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 SMARCD1 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SMARCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0016514 SWI/SNF complex IDA 8804307
GO:0043231 intracellular membrane-bounded organelle IDA --
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:0006337 nucleosome disassembly IDA 8895581
GO:0006338 chromatin remodeling IMP,IDA 12917342
GO:0006357 regulation of transcription from RNA polymerase II promoter NAS 8804307
GO:0007399 nervous system development IEA --
GO:0016569 covalent chromatin modification 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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for SMARCD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMARCD1 Gene:

SMARCD1

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.

Evidence on tissue expression from TISSUES for SMARCD1 Gene

  • Muscle(4.3)
  • Blood(4.1)
  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with SMARCD1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 33
  • 100 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SMARCD1 34 33
  • 95.59 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMARCD1 34 33
  • 94.37 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarcd1 33
  • 93.27 (n)
mouse
(Mus musculus)
Mammalia Smarcd1 16 34 33
  • 93.2 (n)
chicken
(Gallus gallus)
Aves SMARCD1 34 33
  • 81.71 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMARCD1 34
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smarcd1 33
  • 78.54 (n)
Str.7704 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5492 33
zebrafish
(Danio rerio)
Actinopterygii smarcd1 34 33
  • 78.51 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005336 33
  • 66.74 (n)
fruit fly
(Drosophila melanogaster)
Insecta Bap60 35 33 34
  • 64.46 (n)
worm
(Caenorhabditis elegans)
Secernentea swsn-2.1 33
  • 56.55 (n)
ham-3 34
  • 54 (a)
ManyToMany
C18E3.2 35
  • 53 (a)
ZK1128.5 35
  • 53 (a)
swsn-2.2 34
  • 49 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G01890 33
  • 48.78 (n)
rice
(Oryza sativa)
Liliopsida Os04g0382100 33
  • 50.42 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 74 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4313 33
Species where no ortholog for SMARCD1 was found in the sources mined by GeneCards:
  • 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
rs1000005017 -- 50,092,168(+) TCTCT(C/T)TGTCT intron-variant
rs1000062871 -- 50,098,221(+) GTATC(A/G)GTTTG intron-variant
rs1000071579 -- 50,091,057(+) ACCTC(A/G)TGATC intron-variant
rs1000349845 -- 50,092,711(+) TTTGT(G/T)TTTGA intron-variant
rs1000409266 -- 50,094,891(+) TTCCT(A/G)GGTTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMARCD1 Gene

Variant ID Type Subtype PubMed ID
nsv558840 CNV loss 21841781

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMARCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 PW … Archer TK (Molecular and cellular biology 2003) 2 3 4 22 60
  2. Diversity and specialization of mammalian SWI/SNF complexes. (PMID: 8804307) Wang W … Crabtree GR (Genes & development 1996) 2 3 4 60
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  4. Five SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) genes are dispersed in the human genome. (PMID: 9693044) Ring HZ … Francke U (Genomics 1998) 2 3 60
  5. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. (PMID: 8895581) Wang W … Crabtree GR (The EMBO journal 1996) 3 4 60

Products for SMARCD1 Gene

Sources for SMARCD1 Gene

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