Smarcb1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarcb1provided by MGI
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1provided by MGI
Primary source: MGI:MGI:1328366
See related: Ensembl:ENSMUSG00000000902 AllianceGenome:MGI:1328366
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: Ini1; Snf5; Baf47; SNF5/INI1
Summary: Predicted to enable several functions, including Tat protein binding activity; p53 binding activity; and transcription coactivator activity. Predicted to contribute to RNA polymerase I core promoter sequence-specific DNA binding activity. Acts upstream of or within blastocyst hatching; cell differentiation; and negative regulation of cell population proliferation. Located in XY body and nucleus. Part of SWI/SNF complex; nBAF complex; and npBAF complex. Is expressed in several structures, including branchial arch; central nervous system; genitourinary system; limb primordium; and sensory organ. Used to study atypical teratoid rhabdoid tumor. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 3; atypical teratoid rhabdoid tumor; neurilemmomatosis; and rhabdoid cancer. Orthologous to human SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in adrenal adult (RPKM 44.4), CNS E11.5 (RPKM 42.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 38.61 cM

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (75732603..75757448, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (75896769..75921614, complement)

Chromosome 10 - NC_000076.7 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
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?

A Carboxy-terminal Smarcb1 Point Mutation Induces Hydrocephalus Formation and Affects AP-1 and Neuronal Signalling Pathways in Mice.
Title: A Carboxy-terminal Smarcb1 Point Mutation Induces Hydrocephalus Formation and Affects AP-1 and Neuronal Signalling Pathways in Mice.
SMARCB1 regulates the hypoxic stress response in sickle cell trait.
Title: SMARCB1 regulates the hypoxic stress response in sickle cell trait.
Data suggest that SWI-SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 protein (SMARCB1)-mediated remodeling of chromatin landscapes is important for the maintenance and differentiation of embryonic stem cells (ESCs).
Title: Smarcb1 maintains the cellular identity and the chromatin landscapes of mouse embryonic stem cells.
SMARCB1-deficient rhabdoid tumors exhibit dramatic activation of the unfolded protein response and endoplasmic reticulum stress response via a genetically intact MYC-p19(ARF)-p53 axis.
Title: p53 Is a Master Regulator of Proteostasis in SMARCB1-Deficient Malignant Rhabdoid Tumors.
Analyses of the Smarcb1 mutant mice indicate that one prominent midline abnormality, corpus callosum agenesis, is due to midline glia aberrations. Study results establish a novel role of Smarcb1 in the development of the brain midline and have important clinical implications for BAF (BRG1/BRM-associated factor) complex-related intellectual disability/neurodevelopmental disorders.
Title: Mutations in SMARCB1 and in other Coffin-Siris syndrome genes lead to various brain midline defects.
Data show that early Smarcb1 loss causes rhabdoid tumors whereas loss at later stages combined with Nf2 gene inactivation causes shwannomas.
Title: Timing of Smarcb1 and Nf2 inactivation determines schwannoma versus rhabdoid tumor development.
The occurrence of intracranial rhabdoid tumours depends on control of Smarcb1 inactivation.
Title: The occurrence of intracranial rhabdoid tumours in mice depends on temporal control of Smarcb1 inactivation.
These results support recent findings regarding the effectivity of EGFR inhibitors in hindering the proliferation of human MRT cells and demonstrate that activation of EGFR signaling in Rhabdoid tumors is SMARCB1 dependent.
Title: Phosphoproteomic analysis reveals Smarcb1 dependent EGFR signaling in Malignant Rhabdoid tumor cells.
these findings uncover a novel role for Snf5 in oligodendrocyte generation and survival, and they offer evidence of the first genetically engineered mouse model for AT/RT in the CNS.
Title: Generation of a mouse model of atypical teratoid/rhabdoid tumor of the central nervous system through combined deletion of Snf5 and p53.
This study show here that loss of Smarcb1 and Smarca4 leads to severe proliferation deficits of granule neuron precursors and a hypoplastic cerebellum.
Title: Loss of Smarc proteins impairs cerebellar development.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Variation

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Alleles

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

Gene trapped (1) 1 citation
Targeted (10) 1 citation
Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10Jhu68 (e-PCR), detects polymorphism
- UniSTS:158722

NoName (e-PCR)
- UniSTS:236394

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

NoName (e-PCR)
- UniSTS:224663

AA892528 (e-PCR)
- UniSTS:250021

RH136377 (e-PCR)
- UniSTS:210367

Smarcb1 (e-PCR), detects polymorphism
- UniSTS:527555

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
contributes_to RNA polymerase I core promoter sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables Tat protein binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables p53 binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within blastocyst development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blastocyst hatching	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within hepatocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
involved_in nucleosome disassembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation by host of viral transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of double-strand break repair	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of glucose mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of myoblast differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	ISO Inferred from Sequence Orthology more info
involved_in regulation of G0 to G1 transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of G1/S transition of mitotic cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of mitotic metaphase/anaphase transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of nucleotide-excision repair	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within single stranded viral RNA replication via double stranded DNA intermediate	ISO Inferred from Sequence Orthology more info
involved_in transcription initiation-coupled chromatin remodeling	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RSC-type complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
part_of SWI/SNF complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF superfamily-type complex	IDA Inferred from Direct Assay more info	PubMed
located_in XY body	IDA Inferred from Direct Assay more info	PubMed
part_of bBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of brahma complex	IBA Inferred from Biological aspect of Ancestor more info
part_of brahma complex	NAS Non-traceable Author Statement more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
part_of chromatin	NAS Non-traceable Author Statement more info	PubMed
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in kinetochore	NAS Non-traceable Author Statement more info	PubMed
part_of nBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of nBAF complex	IDA Inferred from Direct Assay more info	PubMed
part_of nBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of npBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of npBAF complex	IDA Inferred from Direct Assay more info	PubMed
part_of npBAF complex	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear chromosome	IEA Inferred from Electronic Annotation more info
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nucleolus	ISO Inferred from Sequence Orthology 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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

Names: BRG1-associated factor 47; SNF5 homolog; integrase interactor 1 protein; mSNF5

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_001161853.1 → NP_001155325.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform 2

See identical proteins and their annotated locations for NP_001155325.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AI840539, AK145552, AK150169

Consensus CDS

CCDS48602.1

UniProtKB/TrEMBL

Q3UDA4, Q9ESU0

Related

ENSMUSP00000112463.2, ENSMUST00000121304.2

Conserved Domains (2) summary

pfam04855
Location:172 → 354

SNF5; SNF5 / SMARCB1 / INI1

cd21086
Location:9 → 98

WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins
NM_011418.2 → NP_035548.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform 1

See identical proteins and their annotated locations for NP_035548.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AI840539, AK075906, AK150169

Consensus CDS

CCDS23936.1

UniProtKB/Swiss-Prot

Q9Z0H3

UniProtKB/TrEMBL

Q6ZWP4, Q9ESU1

Related

ENSMUSP00000000925.4, ENSMUST00000000925.10

Conserved Domains (2) summary

pfam04855
Location:181 → 363

SNF5; SNF5 / SMARCB1 / INI1

cd21086
Location:9 → 107

WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins