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SMARCD3 SWI/SNF related BAF chromatin remodeling complex subunit D3 [ Homo sapiens (human) ]

Gene ID: 6604, updated on 19-Sep-2024

Summary

Official Symbol
SMARCD3provided by HGNC
Official Full Name
SWI/SNF related BAF chromatin remodeling complex subunit D3provided by HGNC
Primary source
HGNC:HGNC:11108
See related
Ensembl:ENSG00000082014 MIM:601737; AllianceGenome:HGNC:11108
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
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Genomic context

See SMARCD3 in Genome Data Viewer
Location:
7q36.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (151238780..151277149, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152411900..152450299, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150935866..150974235, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ABCF2-H2BK1 readthrough Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:150910975-150912174 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:150916273-150916470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26854 Neighboring gene ATP binding cassette subfamily F member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150930441-150931006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150932437-150932937 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:150936637-150937836 Neighboring gene uncharacterized LOC124901779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150938593-150939094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150941724-150942298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150942299-150942872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150942873-150943447 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150943448-150944021 Neighboring gene Sharpr-MPRA regulatory region 13648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18809 Neighboring gene chondroitin polymerizing factor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150949301-150950210 Neighboring gene microRNA 671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150953220-150953720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150953721-150954221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150971756-150972555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150974709-150975418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151000420-151001278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26858 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:151038519-151039020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26859 Neighboring gene negative regulator of ubiquitin like proteins 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151084439-151085101 Neighboring gene WD repeat domain 86 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151107690-151108322 Neighboring gene WDR86 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC111010

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables nuclear receptor coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
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
 
enables transcription coregulator binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cardiac right ventricle formation 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 NAS
Non-traceable Author Statement
more info
PubMed 
involved_in muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in neural retina development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in nucleosome disassembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription 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 G2/M transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of T cell differentiation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of cell differentiation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of double-strand break repair NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of myoblast differentiation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of neuroblast proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of G0 to G1 transition NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of G1/S transition of mitotic cell cycle NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of mitotic metaphase/anaphase transition NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of nucleotide-excision repair NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
involved_in secondary heart field specification IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of SWI/SNF complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of SWI/SNF complex NAS
Non-traceable Author Statement
more info
PubMed 
part_of brahma complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin NAS
Non-traceable Author Statement
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
part_of nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
part_of nBAF complex NAS
Non-traceable Author Statement
more info
PubMed 
part_of npBAF complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
part_of npBAF complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in 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
Swp73-like protein
chromatin remodeling complex BAF60C subunit
mammalian chromatin remodeling complex BRG1-associated factor 60C

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.

Genomic

  1. NG_029468.1 RefSeqGene

    Range
    33452..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
    D3DX10, Q2YD86, Q6STE5, Q75MJ2, Q75MR8, Q92926, Q9BUH1
    UniProtKB/TrEMBL
    B3KXL9
    Related
    ENSP00000262188.8, ENST00000262188.13
    Conserved Domains (1) summary
    cd17676
    Location:265338
    SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins
  2. NM_001003802.2NP_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)
    AC021097, AY450431
    Consensus CDS
    CCDS5924.1
    UniProtKB/TrEMBL
    A0A090N8Z9, B3KXL9
    Related
    ENSP00000349254.2, ENST00000356800.6
    Conserved Domains (2) summary
    NF033761
    Location:2108
    gliding_GltJ; adventurous gliding motility protein GltJ
    cl38907
    Location:252325
    SWIB-MDM2; SWIB/MDM2 domain family
  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/TrEMBL
    A0A090N8Z9, B3KXL9
    Related
    ENSP00000376558.2, ENST00000392811.6
    Conserved Domains (2) summary
    NF033761
    Location:2108
    gliding_GltJ; adventurous gliding motility protein GltJ
    cl38907
    Location:252325
    SWIB-MDM2; SWIB/MDM2 domain family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    151238780..151277149 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420758.1XP_047276714.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X2

    UniProtKB/TrEMBL
    B3KXL9
  2. XM_047420757.1XP_047276713.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X1

    UniProtKB/TrEMBL
    B7Z4U8

RNA

  1. XR_007060146.1 RNA Sequence

  2. XR_927518.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    152411900..152450299 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358860.1XP_054214835.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4

    UniProtKB/TrEMBL
    B3KXL9
  2. XM_054358861.1XP_054214836.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X5

    UniProtKB/TrEMBL
    B3KXL9
  3. XM_054358859.1XP_054214834.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X3

    UniProtKB/TrEMBL
    B3KXL9

RNA

  1. XR_008487739.1 RNA Sequence

  2. XR_008487738.1 RNA Sequence