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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
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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)

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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.

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