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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 4-Dec-2022

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; AllianceGenome:HGNC:11106
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
CSS11; 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
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Genomic context

See SMARCD1 in Genome Data Viewer
Location:
12q13.12
Exon count:
14
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50085342..50100707)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50048400..50063789)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50479125..50494490)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr12.1559 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enables molecular adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables transcription coactivator activity NAS
Non-traceable Author Statement
more info
PubMed 
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to fatty acid IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin remodeling IC
Inferred by Curator
more info
PubMed 
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell differentiation IC
Inferred by Curator
more info
PubMed 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in nucleosome disassembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of T cell differentiation IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of cell differentiation IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of cell population proliferation IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of double-strand break repair IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of myoblast differentiation IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of stem cell population maintenance IC
Inferred by Curator
more info
PubMed 
involved_in regulation of G0 to G1 transition IC
Inferred by Curator
more info
PubMed 
involved_in regulation of G1/S transition of mitotic cell cycle IC
Inferred by Curator
more info
PubMed 
involved_in regulation of mitotic metaphase/anaphase transition IC
Inferred by Curator
more info
PubMed 
involved_in regulation of nucleotide-excision repair IC
Inferred by Curator
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IC
Inferred by Curator
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
involved_in transcription initiation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of GBAF complex IC
Inferred by Curator
more info
PubMed 
part_of RSC-type complex IC
Inferred by Curator
more info
PubMed 
part_of SWI/SNF complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of SWI/SNF complex IC
Inferred by Curator
more info
PubMed 
part_of SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of brahma complex IC
Inferred by Curator
more info
PubMed 
located_in chromatin IC
Inferred by Curator
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in kinetochore IC
Inferred by Curator
more info
PubMed 
part_of nBAF complex IC
Inferred by Curator
more info
PubMed 
part_of nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
part_of npBAF complex IC
Inferred by Curator
more info
PubMed 
part_of npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nuclear matrix IC
Inferred by Curator
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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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_003076.5NP_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
    Consensus CDS
    CCDS8797.2
    UniProtKB/Swiss-Prot
    Q96GM5, Q9Y635
    Related
    ENSP00000378414.4, ENST00000394963.9
    Conserved Domains (1) summary
    cd17674
    Location:294370
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins
  2. NM_139071.3NP_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, ENST00000381513.8
    Conserved Domains (1) summary
    cd17674
    Location:294370
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    50085342..50100707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269107.5XP_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 (1) summary
    cd17674
    Location:253329
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins
  2. XM_047429450.1XP_047285406.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X2

  3. XM_011538695.3XP_011536997.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X3

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

RNA

  1. XR_944683.3 RNA Sequence

  2. XR_944684.3 RNA Sequence

  3. XR_007063120.1 RNA Sequence

  4. XR_007063118.1 RNA Sequence

  5. XR_007063119.1 RNA Sequence

  6. XR_007063121.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    50048400..50063789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)