U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

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: 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Alleles

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

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

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

Go to the top of the page Help
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)

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_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

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

Other Literature Sources
Chemical Information
Molecular Biology Databases
Research Materials
Tools