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

Summary

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

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_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Chromatin regulator SMARCAL1 modulates cellular lipid metabolism.
Title: Chromatin regulator SMARCAL1 modulates cellular lipid metabolism.
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.
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.
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.
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.
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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 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 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

EC 3.6.1.-

EC 3.6.4.-

XP_006496204.1

EC 3.6.1.-

EC 3.6.4.-

XP_006496205.1

EC 3.6.1.-

EC 3.6.4.-

XP_006496206.1

EC 3.6.1.-

EC 3.6.4.-

XP_006496207.1

EC 3.6.1.-

EC 3.6.4.-

XP_011236859.1

EC 3.6.1.-

EC 3.6.4.-

XP_030111404.1

EC 3.6.1.-

EC 3.6.4.-

XP_036008323.1

EC 3.6.1.-

EC 3.6.4.-

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)

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

NC_000067.7 Reference GRCm39 C57BL/6J

Range

72575593..72675949

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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)
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)
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)
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)