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    Smarcal1 SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 [ Mus musculus (house mouse) ]

    Gene ID: 54380, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Smarcal1provided by MGI
    Official Full Name
    SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1provided by MGI
    Primary source
    MGI:MGI:1859183
    See related
    Ensembl:ENSMUSG00000039354 AllianceGenome:MGI:1859183
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Mharp; 6030401P21Rik
    Summary
    Enables ATP-dependent activity, acting on DNA. Predicted to be involved in double-strand break repair via nonhomologous end joining; regulation of transcription by RNA polymerase II; and replication fork processing. Predicted to be located in nucleoplasm and site of double-strand break. Predicted to be part of DNA replication factor A complex. Predicted to be active in nuclear replication fork. Is expressed in cerebral cortex and genitourinary system. Used to study Schimke immuno-osseous dysplasia. Human ortholog(s) of this gene implicated in Schimke immuno-osseous dysplasia. Orthologous to human SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in frontal lobe adult (RPKM 6.3), CNS E18 (RPKM 6.3) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Smarcal1 in Genome Data Viewer
    Location:
    1 C3; 1 36.72 cM
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (72575593..72675949)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (72536695..72636790)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_01276 Neighboring gene predicted gene, 39661 Neighboring gene membrane associated ring-CH-type finger 4 Neighboring gene ribosomal protein L17 pseudogene Neighboring gene STARR-seq mESC enhancer starr_01277 Neighboring gene STARR-positive B cell enhancer ABC_E1548 Neighboring gene STARR-seq mESC enhancer starr_01281 Neighboring gene predicted gene, 39662 Neighboring gene ankyrin and armadillo repeat containing Neighboring gene STARR-seq mESC enhancer starr_01283 Neighboring gene ribosomal protein L19 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Chromatin regulator SMARCAL1 modulates cellular lipid metabolism. Nagai TH, et al. Commun Biol, 2023 Dec 21. PMID 38129665, Free PMC Article
    2. SMARCAL1 deficiency predisposes to non-Hodgkin lymphoma and hypersensitivity to genotoxic agents in vivo. Baradaran-Heravi A, et al. Am J Med Genet A, 2012 Sep. PMID 22888040, Free PMC Article
    3. A structure-specific nucleic acid-binding domain conserved among DNA repair proteins. Mason AC, et al. Proc Natl Acad Sci U S A, 2014 May 27. PMID 24821763, Free PMC Article
    4. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Leuzzi G, et al. Cell, 2024 Feb 15. PMID 38301646,
    5. The annealing helicase SMARCAL1 maintains genome integrity at stalled replication forks. Bansbach CE, et al. Genes Dev, 2009 Oct 15. PMID 19793861, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion.
      Title: SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion.
    2. Chromatin regulator SMARCAL1 modulates cellular lipid metabolism.
      Title: Chromatin regulator SMARCAL1 modulates cellular lipid metabolism.
    3. The main roles of SMARCAL1 in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress are reviewed.
      Title: The role of SMARCAL1 in replication fork stability and telomere maintenance.
    4. our data reveal the critical function of the DNA replication stress response and, specifically, Smarcal1 in hematopoietic cell survival and tumor development. Our results also provide important insight into the immunodeficiency observed in individuals with mutations in SMARCAL1 by suggesting that it is an HSPC defect.
      Title: Defective replication stress response inhibits lymphomagenesis and impairs lymphocyte reconstitution.
    5. results provide the first identification, to our knowledge, of an endogenous source of replication stress that requires SMARCAL1 for resolution and define differences between members of this class of replication fork-repair enzymes.
      Title: SMARCAL1 maintains telomere integrity during DNA replication.
    6. the role of SMARCAL1 in the pathogenesis of Schimke immuno-osseous dysplasia
      Title: Insights into the renal pathogenesis in Schimke immuno-osseous dysplasia: A renal histological characterization and expression analysis.
    7. Mutation of predicted DNA-binding residues in the HARP domain dramatically reduced fork binding and regression activities of SMARCAL1 catalytic domain.
      Title: A structure-specific nucleic acid-binding domain conserved among DNA repair proteins.
    8. did not find evidence of defective NER or NHEJ; however, Smarcal1-deficient mice were hypersensitive to several genotoxic agents
      Title: SMARCAL1 deficiency predisposes to non-Hodgkin lymphoma and hypersensitivity to genotoxic agents in vivo.
    9. SMARCAL1 annealing helicase buffers fluctuations in gene expression and that alterations in gene expression contribute to the penetrance of SIOD.
      Title: Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (3)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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
    		  
    enables ATP-dependent DNA/DNA annealing activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ATP-dependent activity, acting on DNA IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA damage response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in replication fork processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in replication fork processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in replication fork processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of DNA replication factor A complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of DNA replication factor A complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nuclear replication fork IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
    Names
    hepA-related protein
    sucrose nonfermenting protein 2-like 1
    NP_061287.2
    XP_006496204.1
    XP_006496205.1
    XP_006496206.1
    XP_006496207.1
    XP_011236859.1
    XP_030111404.1
    XP_036008323.1

    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_018817.2 → NP_061287.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

      See identical proteins and their annotated locations for NP_061287.2

      Status: VALIDATED

      Source sequence(s)
      AC163484, AK083488, AK146767, BY739344
      Consensus CDS
      CCDS35609.1
      UniProtKB/Swiss-Prot
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, Q9QYC4
      Related
      ENSMUSP00000047589.9, ENSMUST00000047615.15
      Conserved Domains (3) summary
      cd18793
      Location:666 → 791
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:395 → 604
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:214 → 268
      HARP; HepA-related protein (HARP)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000067.7 Reference GRCm39 C57BL/6J

      Range
      72575593..72675949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006496141.5 → XP_006496204.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006496204.1

      UniProtKB/Swiss-Prot
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, Q9QYC4
      Conserved Domains (3) summary
      cd18793
      Location:666 → 791
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:395 → 604
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:214 → 268
      HARP; HepA-related protein (HARP)

    2. XM_006496143.5 → XP_006496206.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006496206.1

      UniProtKB/Swiss-Prot
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, Q9QYC4
      Conserved Domains (3) summary
      cd18793
      Location:666 → 791
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:395 → 604
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:214 → 268
      HARP; HepA-related protein (HARP)

    3. XM_011238557.4 → XP_011236859.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X2

      Related
      ENSMUST00000136498.8
      Conserved Domains (3) summary
      cd18793
      Location:666 → 791
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:395 → 604
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:214 → 267
      HARP; HepA-related protein (HARP)

    4. XM_036152430.1 → XP_036008323.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X3

      Conserved Domains (3) summary
      cd18793
      Location:420 → 545
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:149 → 358
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:56 → 110
      HARP; HepA-related protein (HARP)

    5. XM_030255544.2 → XP_030111404.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X4

      Conserved Domains (3) summary
      cd18793
      Location:372 → 497
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:101 → 310
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:8 → 61
      HARP; HepA-related protein (HARP)

    6. XM_006496142.5 → XP_006496205.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006496205.1

      UniProtKB/Swiss-Prot
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, Q9QYC4
      Related
      ENSMUSP00000137833.2, ENSMUST00000152225.2
      Conserved Domains (3) summary
      cd18793
      Location:666 → 791
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:395 → 604
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:214 → 268
      HARP; HepA-related protein (HARP)

    7. XM_006496144.1 → XP_006496207.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006496207.1

      UniProtKB/Swiss-Prot
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, Q9QYC4
      Conserved Domains (3) summary
      cd18793
      Location:666 → 791
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18010
      Location:395 → 604
      DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
      pfam07443
      Location:214 → 268
      HARP; HepA-related protein (HARP)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BJL0.1 GenPept UniProtKB/Swiss-Prot:Q8BJL0

    Gene LinkOut

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