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SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 [ Homo sapiens (human) ]

Gene ID: 6602, updated on 21-Oct-2018

Summary

Official Symbol
SMARCD1provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1provided by HGNC
Primary source
HGNC:HGNC:11106
See related
Ensembl:ENSG00000066117 MIM:601735; Vega:OTTHUMG00000150194
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Rsc6p; BAF60A; CRACD1
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 14.1), testis (RPKM 13.9) and 25 other tissues See more
Orthologs

Genomic context

See SMARCD1 in Genome Data Viewer
Location:
12q13.12
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (50085200..50100711)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50478760..50494494)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Rac GTPase activating protein 1 Neighboring gene acid sensing ion channel subunit 1 Neighboring gene glycerol-3-phosphate dehydrogenase 1 Neighboring gene cytochrome c oxidase assembly factor COX14

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Most of the components of the SWI2/SNF2 chromatin remodeling complex (BRG1/BRM, BAF250, BAF180, BAF170, BAF155, BAF60a, BAF53A, actin and InI) except BRM, BAF155 and BAF57, are identified to interact with HIV-1 Tat in Jurkat cell PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Glucocorticoid receptor regulatory network, organism-specific biosystem (from Pathway Interaction Database)
    Glucocorticoid receptor regulatory network, organism-specific biosystem
    Glucocorticoid receptor regulatory network
  • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
    RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex scaffold activity IDA
Inferred from Direct Assay
more info
PubMed 
signaling receptor binding IEA
Inferred from Electronic Annotation
more info
 
transcription coactivator activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cellular response to fatty acid IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin-mediated maintenance of transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
nucleosome disassembly IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Names
60 kDa BRG-1/Brm-associated factor subunit A
BRG1-associated factor 60A
SWI/SNF complex 60 kDa subunit A
Swp73-like protein
chromatin remodeling complex BAF60A subunit
mammalian chromatin remodeling complex BRG1-associated factor 60A

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_003076.4NP_003067.3  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform a

    See identical proteins and their annotated locations for NP_003067.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the longer transcript and encodes the full-length isoform (a).
    Source sequence(s)
    AA610093, BC009368, DB010252
    Consensus CDS
    CCDS8797.2
    UniProtKB/Swiss-Prot
    Q96GM5
    Related
    ENSP00000378414.4, OTTHUMP00000196567, ENST00000394963.8, OTTHUMT00000316759
    Conserved Domains (2) summary
    smart00151
    Location:291367
    SWIB; SWI complex, BAF60b domains
    pfam02084
    Location:3998
    Bindin; Bindin
  2. NM_139071.2NP_620710.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform b

    See identical proteins and their annotated locations for NP_620710.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform b), compared to isoform a.
    Source sequence(s)
    AA610093, AC025154, BE905082, CN272379, DA825057, DB010252, N75126
    Consensus CDS
    CCDS8798.2
    UniProtKB/Swiss-Prot
    Q96GM5
    Related
    ENSP00000370924.4, OTTHUMP00000196568, ENST00000381513.8, OTTHUMT00000316760
    Conserved Domains (2) summary
    smart00151
    Location:291367
    SWIB; SWI complex, BAF60b domains
    pfam02084
    Location:3998
    Bindin; Bindin

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    50085200..50100711
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269107.4XP_005269164.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X1

    See identical proteins and their annotated locations for XP_005269164.2

    Conserved Domains (2) summary
    smart00151
    Location:250326
    SWIB; SWI complex, BAF60b domains
    pfam02084
    Location:3998
    Bindin; Bindin
  2. XM_011538695.2XP_011536997.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X2

    Conserved Domains (1) summary
    pfam02084
    Location:3998
    Bindin; Bindin

RNA

  1. XR_944683.2 RNA Sequence

  2. XR_944684.2 RNA Sequence

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