U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Smarca1 SNF2 related chromatin remodeling ATPase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317575, updated on 27-Nov-2024

    Summary

    Official Symbol
    Smarca1provided by RGD
    Official Full Name
    SNF2 related chromatin remodeling ATPase 1provided by RGD
    Primary source
    RGD:1561046
    See related
    EnsemblRapid:ENSRNOG00000003762 AllianceGenome:RGD:1561046
    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
    Also known as
    RGD1561046
    Summary
    Predicted to enable several functions, including ATP-dependent DNA/DNA annealing activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and nucleosome array spacer activity. Predicted to contribute to ATP-dependent chromatin remodeler activity. Predicted to be involved in heterochromatin formation; neuron differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within brain development and regulation of neural precursor cell proliferation. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of CERF complex and NURF complex. Predicted to be active in nucleus. Orthologous to human SMARCA1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 300.5), Brain (RPKM 70.2) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Smarca1 in Genome Data Viewer
    Location:
    Xq35
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (131858148..131944639, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (126980201..127066385, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (134634651..134719503, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene BTB domain containing 10, pseudogene 1 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene karyopherin subunit alpha 1, pseudogene 7 Neighboring gene OCRL, inositol polyphosphate-5-phosphatase

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent DNA/DNA annealing activity ISO
    Inferred from Sequence Orthology
    more info
     
    contributes_to ATP-dependent activity, acting on DNA ISO
    Inferred from Sequence Orthology
    more info
     
    contributes_to ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables nucleosome array spacer activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables nucleosome binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
     
    acts_upstream_of_or_within brain development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of ATPase complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of CERF complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of NURF complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in intracellular membrane-bounded organelle 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
     
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    probable global transcription activator SNF2L1
    Names
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1

    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.

    mRNA and Protein(s)

    1. NM_001271190.1NP_001258119.1  probable global transcription activator SNF2L1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6JMN9, D3ZIE5
      Related
      ENSRNOP00000060122.5, ENSRNOT00000068478.5
      Conserved Domains (7) summary
      PLN03142
      Location:641061
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd00046
      Location:207346
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00167
      Location:851890
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
      pfam00271
      Location:489604
      Helicase_C; Helicase conserved C-terminal domain
      pfam09110
      Location:750848
      HAND; HAND
      pfam09111
      Location:9051017
      SLIDE; SLIDE
      pfam13892
      Location:96114
      DBINO; DNA-binding domain

    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_086039.1 Reference GRCr8

      Range
      131858148..131944639 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006257526.5XP_006257588.3  probable global transcription activator SNF2L1 isoform X3

      UniProtKB/TrEMBL
      A6JMN9
    2. XM_063280088.1XP_063136158.1  probable global transcription activator SNF2L1 isoform X5

      Related
      ENSRNOP00000103474.1, ENSRNOT00000139301.1
    3. XM_063280086.1XP_063136156.1  probable global transcription activator SNF2L1 isoform X1

      UniProtKB/TrEMBL
      D3ZIE5
    4. XM_063280087.1XP_063136157.1  probable global transcription activator SNF2L1 isoform X2

    5. XM_006257525.5XP_006257587.3  probable global transcription activator SNF2L1 isoform X2

      UniProtKB/TrEMBL
      A6JMN9
      Related
      ENSRNOP00000104293.1, ENSRNOT00000155509.1
    6. XM_006257527.5XP_006257589.3  probable global transcription activator SNF2L1 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AH59, A6JMN9
      Related
      ENSRNOP00000077868.2, ENSRNOT00000115795.2

    RNA

    1. XR_010061202.1 RNA Sequence