Smarcb1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Smarcb1provided by RGD
Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1provided by RGD
Primary source: RGD:1308761
See related: EnsemblRapid:ENSRNOG00000028302 AllianceGenome:RGD:1308761
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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. Predicted to be involved in several processes, including chromatin remodeling; positive regulation by host of viral transcription; and regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including blastocyst hatching; hepatocyte differentiation; and single stranded viral RNA replication via double stranded DNA intermediate. Located in chromatin. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 3; central nervous system cancer (multiple); rhabdoid cancer; and schwannomatosis (multiple). Orthologous to human SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Testes (RPKM 105.5), Brain (RPKM 78.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (12740105..12763054)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (12741164..12763616)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (13679955..13702821)

Chromosome 20 - NC_086038.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These findings indicate that the decreased level of Snf5 binding to the promoter region of the Oct4 gene down-regulated the expression of Oct4, which may be the mechanism underlying the decline in osteogenic capacities in replicative senescent BMSCs.
Title: The role of Snf5 in the osteogenic differentiation potential during replicative senescence of rat mesenchymal stromal cells.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

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

Gene Ontology Provided by RGD

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
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within blastocyst development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blastocyst hatching	ISO Inferred from Sequence Orthology 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
acts_upstream_of_or_within hepatocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glucose mediated signaling pathway	ISO Inferred from Sequence Orthology 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 of nucleolar large rRNA by RNA polymerase I	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
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 SWI/SNF complex	ISO Inferred from Sequence Orthology more info
located_in XY body	ISO Inferred from Sequence Orthology more info
part_of brahma complex	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in fibrillar center	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in germ cell nucleus	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
part_of nBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of nBAF complex	ISO Inferred from Sequence Orthology more info
part_of npBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of npBAF complex	ISO Inferred from Sequence Orthology more info
located_in nuclear chromosome	IEA Inferred from Electronic Annotation more info
located_in nucleolus	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
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

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_001025728.1 → NP_001020899.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

See identical proteins and their annotated locations for NP_001020899.1

Status: PROVISIONAL

Source sequence(s)

BC099195

UniProtKB/TrEMBL

A0A8J8YH81, G3V935, Q4KLI0

Related

ENSRNOP00000100193.1, ENSRNOT00000171447.1

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086038.1 Reference GRCr8

Range

12740105..12763054

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006256318.5 → XP_006256380.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform X1

See identical proteins and their annotated locations for XP_006256380.1

UniProtKB/TrEMBL

A0A8J8YH81, A6JKF4

Related

ENSRNOP00000034916.7, ENSRNOT00000029458.8

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
XM_063279245.1 → XP_063135315.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform X2