U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Smarcb1 SWI/SNF related BAF chromatin remodeling complex subunit B1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361825, updated on 27-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Smarcb1provided by RGD
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit B1provided by RGD
    Primary source
    RGD:1308761
    See related
    EnsemblRapid:ENSRNOG00000028302 AllianceGenome:RGD:1308761
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including Tat protein binding activity; p53 binding activity; and transcription coactivator activity. Predicted to contribute to RNA polymerase I core promoter sequence-specific DNA binding activity. Predicted to be involved in several processes, including chromatin remodeling; positive regulation by host of viral transcription; and regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including blastocyst hatching; hepatocyte differentiation; and single stranded viral RNA replication via double stranded DNA intermediate. Located in chromatin. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 3; meningioma; rhabdoid cancer; rhabdoid tumor predisposition syndrome 1; and schwannomatosis (multiple). Orthologous to human SMARCB1 (SWI/SNF related BAF chromatin remodeling complex subunit B1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 105.5), Brain (RPKM 78.2) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Smarcb1 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (12740105..12763054)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (12741164..12763616)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (13679955..13702821)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene similar to human chromosome 22 open reading frame 15 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 10 Neighboring gene matrix metallopeptidase 11 Neighboring gene uncharacterized LOC134483889 Neighboring gene derlin 3 Neighboring gene macrophage migration inhibitory factor Neighboring gene uncharacterized LOC134483888

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. SMARCB1 (INI1)-deficient sinonasal carcinoma: a series of 13 cases with assessment of histologic patterns. Kakkar A, et al. Hum Pathol, 2019 Jan. PMID 30120966
    2. The role of Snf5 in the osteogenic differentiation potential during replicative senescence of rat mesenchymal stromal cells. Wu S, et al. Mech Ageing Dev, 2018 Apr. PMID 29398003
    3. The SWI/SNF Subunit INI1 Contains an N-Terminal Winged Helix DNA Binding Domain that Is a Target for Mutations in Schwannomatosis. Allen MD, et al. Structure, 2015 Jul 7. PMID 26073604, Free PMC Article
    4. Loss of INI1 expression is characteristic of both conventional and proximal-type epithelioid sarcoma. Hornick JL, et al. Am J Surg Pathol, 2009 Apr. PMID 19033866
    5. Disruption of Ini1 leads to peri-implantation lethality and tumorigenesis in mice. Guidi CJ, et al. Mol Cell Biol, 2001 May. PMID 11313485, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC116367

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to RNA polymerase I core promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables Tat protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables p53 binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA polymerase I preinitiation complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within blastocyst development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within blastocyst hatching ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hepatocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleosome disassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation by host of viral transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of glucose mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within single stranded viral RNA replication via double stranded DNA intermediate ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription initiation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in XY body ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of brahma complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in germ cell nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of npBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of npBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
    Names
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    mRNA and Protein(s)

    1. NM_001025728.2 → NP_001020899.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform 2

      See identical proteins and their annotated locations for NP_001020899.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      A0A8J8YH81, G3V935, Q4KLI0
      Related
      ENSRNOP00000100193.1, ENSRNOT00000171447.1
      Conserved Domains (2) summary
      pfam04855
      Location:172 → 354
      SNF5; SNF5 / SMARCB1 / INI1
      cd21086
      Location:9 → 98
      WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins

    2. NM_001434638.1 → NP_001421567.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      A0A8J8YH81, A6JKF4

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086038.1 Reference GRCr8

      Range
      12740105..12763054
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006256318.5 → XP_006256380.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform X1

      Related
      ENSRNOP00000034916.7, ENSRNOT00000029458.8
      Conserved Domains (2) summary
      pfam04855
      Location:181 → 363
      SNF5; SNF5 / SMARCB1 / INI1
      cd21086
      Location:9 → 107
      WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins

    2. XM_063279245.1 → XP_063135315.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform X2

      UniProtKB/TrEMBL
      A0A8J8YH81
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools