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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 9-Jun-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMARCD3 in Genome Data Viewer
    Location:
    7q36.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (151238780..151277149, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152411900..152450299, complement)
    105.20220307 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
    • 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 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 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 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 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin NAS
    Non-traceable Author Statement
    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
    Swp73-like protein
    chromatin remodeling complex BAF60C subunit
    mammalian chromatin remodeling complex BRG1-associated factor 60C

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_2023_10

    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