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SMARCD3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [ Homo sapiens (human) ]

Gene ID: 6604, updated on 1-Jun-2020

Summary

Official Symbol
SMARCD3provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3provided by HGNC
Primary source
HGNC:HGNC:11108
See related
Ensembl:ENSG00000082014 MIM:601737
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; BAF60C; CRACD3
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. 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]
Expression
Ubiquitous expression in brain (RPKM 23.8), heart (RPKM 18.1) and 23 other tissues See more
Orthologs

Genomic context

See SMARCD3 in Genome Data Viewer
Location:
7q36.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (151238780..151277452, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150936059..150974231, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ABCF2-H2BE1 readthrough Neighboring gene ATP binding cassette subfamily F member 2 Neighboring gene chondroitin polymerizing factor 2 Neighboring gene microRNA 671 Neighboring gene negative regulator of ubiquitin like proteins 1 Neighboring gene WD repeat domain 86 Neighboring gene WDR86 antisense RNA 1

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?

Phenotypes

NHGRI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC111010

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
nuclear hormone receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity NAS
Non-traceable Author Statement
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cardiac right ventricle formation IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IC
Inferred by Curator
more info
PubMed 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
neural retina development IEP
Inferred from Expression Pattern
more info
PubMed 
nucleosome disassembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of G2/M transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuroblast proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of lipid metabolic process TAS
Traceable Author Statement
more info
 
regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
secondary heart field specification IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
SWI/SNF complex NAS
Non-traceable Author Statement
more info
PubMed 
nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
npBAF complex IDA
Inferred from Direct Assay
more info
PubMed 
npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3
Names
60 kDa BRG-1/Brm-associated factor subunit C
BRG1-associated factor 60C
SWI/SNF complex 60 kDa subunit C
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3, isoform 1
Swp73-like protein
chromatin remodeling complex BAF60C subunit
mammalian chromatin remodeling complex BRG1-associated factor 60C

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.

Genomic

  1. NG_029468.1 RefSeqGene

    Range
    4997..43366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001003801.2NP_001003801.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 2

    See identical proteins and their annotated locations for NP_001003801.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as hBAF60c2, has an alternate 5' sequence, as compared to variant 1. The encoded isoform 2 has a longer and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AC005486, AC021097, AY450430
    Consensus CDS
    CCDS34780.1
    UniProtKB/Swiss-Prot
    Q6STE5
    Related
    ENSP00000262188.8, ENST00000262188.12
    Conserved Domains (3) summary
    smart00151
    Location:259335
    SWIB; SWI complex, BAF60b domains
    pfam07271
    Location:2767
    Cytadhesin_P30; Cytadhesin P30/P32
    pfam13388
    Location:28138
    DUF4106; Protein of unknown function (DUF4106)
  2. NM_001003802.1NP_001003802.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 1

    See identical proteins and their annotated locations for NP_001003802.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as hBAF60c1, encodes the shorter isoform (1). Both variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AY450431
    Consensus CDS
    CCDS5924.1
    UniProtKB/Swiss-Prot
    Q6STE5
    UniProtKB/TrEMBL
    A0A090N8Z9
    Related
    ENSP00000349254.2, ENST00000356800.6
    Conserved Domains (3) summary
    smart00151
    Location:246322
    SWIB; SWI complex, BAF60b domains
    pfam07271
    Location:354
    Cytadhesin_P30; Cytadhesin P30/P32
    pfam13388
    Location:7125
    DUF4106; Protein of unknown function (DUF4106)
  3. NM_003078.4NP_003069.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 1

    See identical proteins and their annotated locations for NP_003069.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' exon, but encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC005486, AC021097, BC002628, BI598614, U66619
    Consensus CDS
    CCDS5924.1
    UniProtKB/Swiss-Prot
    Q6STE5
    UniProtKB/TrEMBL
    A0A090N8Z9
    Related
    ENSP00000376558.2, ENST00000392811.6
    Conserved Domains (3) summary
    smart00151
    Location:246322
    SWIB; SWI complex, BAF60b domains
    pfam07271
    Location:354
    Cytadhesin_P30; Cytadhesin P30/P32
    pfam13388
    Location:7125
    DUF4106; Protein of unknown function (DUF4106)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    151238780..151277452 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446887.1XP_024302655.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X2

    Conserved Domains (3) summary
    smart00151
    Location:246322
    SWIB; SWI complex, BAF60b domains
    pfam07271
    Location:354
    Cytadhesin_P30; Cytadhesin P30/P32
    pfam13388
    Location:7125
    DUF4106; Protein of unknown function (DUF4106)
  2. XM_011516521.2XP_011514823.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4

    See identical proteins and their annotated locations for XP_011514823.1

    Conserved Domains (2) summary
    COG5531
    Location:77274
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    cl38907
    Location:163236
    SWIB-MDM2; SWIB/MDM2 domain family
  3. XM_024446888.1XP_024302656.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X3

    Conserved Domains (1) summary
    smart00151
    Location:157233
    SWIB; SWI complex, BAF60b domains
  4. XM_024446889.1XP_024302657.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X5

    Conserved Domains (1) summary
    smart00151
    Location:94170
    SWIB; SWI complex, BAF60b domains
  5. XM_024446886.1XP_024302654.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X1

    Conserved Domains (3) summary
    smart00151
    Location:259335
    SWIB; SWI complex, BAF60b domains
    pfam07271
    Location:2767
    Cytadhesin_P30; Cytadhesin P30/P32
    pfam13388
    Location:28138
    DUF4106; Protein of unknown function (DUF4106)
  6. XM_024446890.1XP_024302658.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X6

    Conserved Domains (1) summary
    smart00151
    Location:94170
    SWIB; SWI complex, BAF60b domains

RNA

  1. XR_927517.1 RNA Sequence

  2. XR_001744856.1 RNA Sequence

  3. XR_927518.1 RNA Sequence

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