Human Gene SMARCD3 (uc010lqa.1) Description and Page Index
  Description: Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 (SMARCD3), transcript variant 3, mRNA.
RefSeq Summary (NM_001003801): 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. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr7:150,938,344-150,945,749 Size: 7,406 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr7:150,938,813-150,945,648 Size: 6,836 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:150,938,344-150,945,749)mRNA (may differ from genome)Protein (308 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SMRD3_HUMAN
DESCRIPTION: RecName: Full=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3; AltName: Full=60 kDa BRG-1/Brm-associated factor subunit C; AltName: Full=BRG1-associated factor 60C; Short=BAF60C;
FUNCTION: Plays a role in ATP dependent nucleosome remodeling by SMARCA4 containing complexes. Stimulates nuclear receptor mediated transcription. 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).
SUBUNIT: 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. Interacts with SMARCA4/BRG1/BAF190A, the catalytic subunit of the SWI/SNF related nucleosome-remodeling complexes BRG1(I) and BRG1(II). The precise distribution of the related SMARCD1, SMARCD2 and SMARCD3 proteins among these and other SWI/SNF nucleosome-remodeling complexes is not fully known. Also interacts with several nuclear receptors including PPARG/NR1C3, RXRA/NR1F1, ESR1, NR5A1, NR5A2/LRH1 and other transcriptional activators including the HLH protein SREBF1/SREBP1 and the homeobox protein PBX1. May allow recruitment of Swi/SNF containing complexes specifically to promoters where these factors are located. 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).
INTERACTION: P37231:PPARG; NbExp=3; IntAct=EBI-488511, EBI-781384;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Isoform 2 and isoform 1 are expressed in brain, heart, kidney, placenta, prostate, salivary gland, spleen, testis, thyroid, trachea and uterus. Isoform 1 is also expressed in skeletal muscle and adipose tissue.
SIMILARITY: Belongs to the SMARCD family.
SIMILARITY: Contains 1 SWIB domain.
SEQUENCE CAUTION: Sequence=AAC50697.1; Type=Frameshift; Positions=41, 65, 78;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 51.20 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 1118.03 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.60101-0.125 Picture PostScript Text
3' UTR -169.77469-0.362 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019835 - SWIB_domain
IPR003121 - SWIB_MDM2_domain

ModBase Predicted Comparative 3D Structure on Q6STE5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
     SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0003713 transcription coactivator activity
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0016922 ligand-dependent nuclear receptor binding
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity
GO:0035257 nuclear hormone receptor binding

Biological Process:
GO:0002052 positive regulation of neuroblast proliferation
GO:0003007 heart morphogenesis
GO:0003139 secondary heart field specification
GO:0003219 cardiac right ventricle formation
GO:0003407 neural retina development
GO:0006325 chromatin organization
GO:0006337 nucleosome disassembly
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007399 nervous system development
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0019216 regulation of lipid metabolic process
GO:0042692 muscle cell differentiation
GO:0043393 regulation of protein binding
GO:0045893 positive regulation of transcription, DNA-templated
GO:0051152 positive regulation of smooth muscle cell differentiation

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016514 SWI/SNF complex
GO:0071564 npBAF complex
GO:0071565 nBAF complex


-  Descriptions from all associated GenBank mRNAs
  LF206789 - JP 2014500723-A/14292: Polycomb-Associated Non-Coding RNAs.
AY450430 - Homo sapiens 60kDa BRG-1/Brm associated factor subunit c isoform 2 (SMARCD3) mRNA, complete cds.
BC110350 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3, mRNA (cDNA clone MGC:111010 IMAGE:5212363), complete cds.
AY450431 - Homo sapiens 60kDa BRG-1/Brm associated factor subunit c isoform 1 (SMARCD3) mRNA, complete cds.
BC002628 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3, mRNA (cDNA clone MGC:3653 IMAGE:3608512), complete cds.
BX648385 - Homo sapiens mRNA; cDNA DKFZp686H22205 (from clone DKFZp686H22205).
AK127595 - Homo sapiens cDNA FLJ45690 fis, clone FCBBF5000384, highly similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily Dmember 3.
U66619 - Human SWI/SNF complex 60 KDa subunit (BAF60c) mRNA, complete cds.
KJ905318 - Synthetic construct Homo sapiens clone ccsbBroadEn_14843 SMARCD3 gene, encodes complete protein.
AB464257 - Synthetic construct DNA, clone: pF1KB8204, Homo sapiens SMARCD3 gene for SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3, without stop codon, in Flexi system.
JD021805 - Sequence 2829 from Patent EP1572962.
AK316173 - Homo sapiens cDNA, FLJ79072 complete cds, highly similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3.
AK297876 - Homo sapiens cDNA FLJ52707 complete cds, highly similar to SWI/SNF-related matrix-associatedactin-dependent regulator of chromatin subfamily D member 3.
AK309500 - Homo sapiens cDNA, FLJ99541.
LF357878 - JP 2014500723-A/165381: Polycomb-Associated Non-Coding RNAs.
CU678072 - Synthetic construct Homo sapiens gateway clone IMAGE:100023470 5' read SMARCD3 mRNA.
LF357879 - JP 2014500723-A/165382: Polycomb-Associated Non-Coding RNAs.
JD025744 - Sequence 6768 from Patent EP1572962.
MA442366 - JP 2018138019-A/14292: Polycomb-Associated Non-Coding RNAs.
MA593455 - JP 2018138019-A/165381: Polycomb-Associated Non-Coding RNAs.
MA593456 - JP 2018138019-A/165382: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6STE5 (Reactome details) participates in the following event(s):

R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-3215448 SWI/SNF chromatin remodelling complex enhances MEP50:PRMT5 methyltransferase activity
R-HSA-8938217 RUNX1 binds the SWI/SNF complex
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-556833 Metabolism of lipids
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-1430728 Metabolism
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-4839726 Chromatin organization
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: AK309500, BAF60C, D3DX10, Q2YD86, Q6STE5, Q75MJ2, Q75MR8, Q92926, Q9BUH1, SMRD3_HUMAN
UCSC ID: uc010lqa.1
RefSeq Accession: NM_001003801
Protein: Q6STE5 (aka SMRD3_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK309500.1
exon count: 7CDS single in 3' UTR: no RNA size: 1482
ORF size: 927CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2054.00frame shift in genome: no % Coverage: 99.87
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 619# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.