Smarca1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarca1provided by MGI
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1provided by MGI
Primary source: MGI:MGI:1935127
See related: Ensembl:ENSMUSG00000031099 AllianceGenome:MGI:1935127
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: Snf2l; 5730494M04Rik
Summary: Enables chromatin binding activity. Involved in neuron differentiation. Acts upstream of or within brain development and regulation of neural precursor cell proliferation. Located in chromatin. Is active in nucleus. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; limb; and sensory organ. 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: Broad expression in placenta adult (RPKM 7.5), CNS E18 (RPKM 6.6) and 15 other tissues See more
Orthologs: human all
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Genomic context

Location:: X A4; X 25.41 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (46898247..46981490, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (47809370..47892613, complement)

Chromosome X - NC_000086.8 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?

These results begin to establish a role for SNF2L in the precise coordination of gene expression in granulosa cells during folliculogenesis and its broader implications in fertility.
Title: The imitation switch ATPase Snf2l is required for superovulation and regulates Fgl2 in differentiating mouse granulosa cells.
Cancers are sensitive to SNF2L knockdown because, unlike their normal counterparts, they lack sufficient compensation from other family members.
Title: Inhibition of expression of the chromatin remodeling gene, SNF2L, selectively leads to DNA damage, growth inhibition, and cancer cell death.
The imitation switch protein SNF2L regulates steroidogenic acute regulatory protein expression during terminal differentiation of ovarian granulosa cells.
Title: The imitation switch protein SNF2L regulates steroidogenic acute regulatory protein expression during terminal differentiation of ovarian granulosa cells.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (4)
Targeted (2) 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
contributes_to ATP-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology more info
contributes_to ATP-dependent activity, acting on DNA	ISS Inferred from Sequence or Structural Similarity 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	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
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
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	NAS Non-traceable Author Statement more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity 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 positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of neural precursor cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of neural precursor cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed

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	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: probable global transcription activator SNF2L1

Names: ATP-dependent helicase SMARCA1; DNA-dependent ATPase SNF2L; nucleosome-remodeling factor subunit SNF2L

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_001290708.2 → NP_001277637.1 probable global transcription activator SNF2L1 isoform 2

See identical proteins and their annotated locations for NP_001277637.1

Status: VALIDATED

Source sequence(s)

AK030741, AL671903, BC057115

Consensus CDS

CCDS72374.1

UniProtKB/TrEMBL

Q05DE7

Related

ENSMUSP00000099138.3, ENSMUST00000101616.9

Conserved Domains (7) summary

PLN03142
Location:2 → 1061

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd00046
Location:207 → 346

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:851 → 890

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:489 → 604

Helicase_C; Helicase conserved C-terminal domain

pfam09110
Location:750 → 848

HAND; HAND

pfam09111
Location:905 → 1017

SLIDE; SLIDE

pfam13892
Location:73 → 114

DBINO; DNA-binding domain
NM_001358618.1 → NP_001345547.1 probable global transcription activator SNF2L1 isoform 3

Status: VALIDATED

Source sequence(s)

AL671903

UniProtKB/TrEMBL

Q05DE7

Conserved Domains (2) summary

pfam13892
Location:52 → 109

DBINO; DNA-binding domain

cl26465
Location:86 → 1056

SNF2_N; SNF2 family N-terminal domain
NM_001358619.1 → NP_001345548.1 probable global transcription activator SNF2L1 isoform 1

Status: VALIDATED

Source sequence(s)

AL671903

Consensus CDS

CCDS30104.1

UniProtKB/Swiss-Prot

B1AUP6, B1AUP7, Q6PGB8, Q8BSS1, Q91Y58

UniProtKB/TrEMBL

Q05DE7

Related

ENSMUSP00000086366.5, ENSMUST00000088973.11

Conserved Domains (1) summary

cl26465
Location:2 → 1038

SNF2_N; SNF2 family N-terminal domain
NM_053123.5 → NP_444353.3 probable global transcription activator SNF2L1 isoform 1

See identical proteins and their annotated locations for NP_444353.3

Status: VALIDATED

Source sequence(s)

AK030741, AL671903, BC057115

Consensus CDS

CCDS30104.1

UniProtKB/Swiss-Prot

B1AUP6, B1AUP7, Q6PGB8, Q8BSS1, Q91Y58

UniProtKB/TrEMBL

Q05DE7

Related

ENSMUSP00000076769.5, ENSMUST00000077569.11

Conserved Domains (1) summary

cl26465
Location:2 → 1038

SNF2_N; SNF2 family N-terminal domain

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_000086.8 Reference GRCm39 C57BL/6J

Range

46898247..46981490 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017318646.3 → XP_017174135.1 probable global transcription activator SNF2L1 isoform X1

UniProtKB/TrEMBL

Q05DE7

Conserved Domains (2) summary

PLN03142
Location:86 → 1033

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

pfam13892
Location:52 → 109

DBINO; DNA-binding domain