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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
  • BAF60A 3 4 6
  • 60 KDa BRG-1/Brm-Associated Factor Subunit A 3 4
  • BRG1-Associated Factor 60A 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

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 Glucocorticoid receptor regulatory network and Transcription Ligand-dependent activation of the ESR1/SP 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

Genomic Location for SMARCD1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMARCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMARCD1 Gene

Regulatory Elements 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

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys101, Lys156, Lys223, and Lys464

Other Protein References for SMARCD1 Gene

No data available for DME Specific Peptides for SMARCD1 Gene

Domains for SMARCD1 Gene

Protein Domains for SMARCD1 Gene

UniProtKB/Swiss-Prot:

SMRD1_HUMAN
Domain:
  • Contains 1 SWIB domain.:
    • Q96GM5
Family:
  • Belongs to the SMARCD family.:
    • Q96GM5
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:0003713 transcription coactivator activity NAS 8804307
GO:0005515 protein binding IPI 12917342
GO:0032947 protein complex scaffold IDA 12917342
genes like me logo Genes that share ontologies with SMARCD1: view

Phenotypes for SMARCD1 Gene

GenomeRNAi human phenotypes for SMARCD1:
genes like me logo Genes that share phenotypes with SMARCD1: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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:0016514 SWI/SNF complex IDA 11078522
GO:0071564 npBAF complex ISS --
GO:0071565 nBAF complex ISS --
genes like me logo Genes that share ontologies with SMARCD1: view

Pathways for SMARCD1 Gene

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

Pathways by source for SMARCD1 Gene

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 12917342
GO:0006357 regulation of transcription from RNA polymerase II promoter NAS 8804307
GO:0007399 nervous system development IEA --
GO:0048096 chromatin-mediated maintenance of transcription IMP 12917342
genes like me logo Genes that share ontologies with SMARCD1: view

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:

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with SMARCD1: view

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 36
  • 100 (n)
  • 100 (a)
SMARCD1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMARCD1 36
  • 94.37 (n)
  • 98.83 (a)
SMARCD1 37
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMARCD1 36
  • 95.59 (n)
  • 99.37 (a)
SMARCD1 37
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smarcd1 36
  • 93.2 (n)
  • 99.42 (a)
Smarcd1 16
Smarcd1 37
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarcd1 36
  • 93.27 (n)
  • 99.81 (a)
chicken
(Gallus gallus)
Aves SMARCD1 36
  • 81.71 (n)
  • 94.34 (a)
SMARCD1 37
  • 95 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMARCD1 37
  • 96 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.5492 36
tropical clawed frog
(Silurana tropicalis)
Amphibia smarcd1 36
  • 78.54 (n)
  • 94.09 (a)
Str.7704 36
zebrafish
(Danio rerio)
Actinopterygii smarcd1 36
  • 78.51 (n)
  • 93.62 (a)
smarcd1 37
  • 88 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005336 36
  • 66.74 (n)
  • 74.94 (a)
fruit fly
(Drosophila melanogaster)
Insecta Bap60 36
  • 64.46 (n)
  • 71.58 (a)
Bap60 37
  • 63 (a)
OneToMany
Bap60 38
  • 78 (a)
worm
(Caenorhabditis elegans)
Secernentea ham-3 37
  • 54 (a)
ManyToMany
swsn-2.1 36
  • 56.55 (n)
  • 58.42 (a)
swsn-2.2 37
  • 49 (a)
ManyToMany
ZK1128.5 38
  • 53 (a)
C18E3.2 38
  • 53 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G01890 36
  • 48.78 (n)
  • 38.48 (a)
rice
(Oryza sativa)
Liliopsida Os04g0382100 36
  • 50.42 (n)
  • 39.62 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4313 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 74 (a)
ManyToMany
-- 37
  • 50 (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

Selected 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 MAF
rs646782 -- 50,088,428(-) AATGG(A/G)AAAAA intron-variant
rs836170 -- 50,095,487(+) acgcc(C/T)ggcta intron-variant
rs836172 -- 50,096,316(+) agaaa(C/G)ggtag intron-variant
rs836175 -- 50,097,784(+) TACCC(A/G)GGAGG intron-variant
rs836181 -- 50,090,820(+) tttgt(A/G/T)ctttt intron-variant

Relevant External Links for SMARCD1 Gene

HapMap Linkage Disequilibrium report
SMARCD1

No data available for Structural Variations from Database of Genomic Variants (DGV) for SMARCD1 Gene

Disorders for SMARCD1 Gene

(1) University of Copenhagen DISEASES for SMARCD1 Gene

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

No data available for UniProtKB/Swiss-Prot 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
  2. Diversity and specialization of mammalian SWI/SNF complexes. (PMID: 8804307) Wang W. … Crabtree G.R. (Genes Dev. 1996) 2 3 4
  3. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. (PMID: 8895581) Wang W. … Crabtree G.R. (EMBO J. 1996) 3 4
  4. 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
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for SMARCD1 Gene

Sources for SMARCD1 Gene

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