Smarca2 SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smarca2provided by RGD
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2provided by RGD
Primary source: RGD:1302988
See related: EnsemblRapid:ENSRNOG00000011931 AllianceGenome:RGD:1302988
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables chromatin binding activity. Involved in spermatid development. Predicted to be located in chromatin; intermediate filament cytoskeleton; and nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Nicolaides-Baraitser syndrome and blepharophimosis-impaired intellectual development syndrome. Orthologous to human SMARCA2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 144.5), Brain (RPKM 123.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q52

Exon count:: 44

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (233617277..233784908)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (224191125..224358640)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (244615811..244783736)

Chromosome 1 - NC_086019.1 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
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?

Brm/Smarca2 regulates the differentiation of early retinal stem cells/progenitors by influencing Brn3b expression and Notch signaling
Title: SWI/SNF chromatin remodeling ATPase Brm regulates the differentiation of early retinal stem cells/progenitors by influencing Brn3b expression and Notch signaling.

Submit: New GeneRIF Correction

General gene information

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Markers

D1Rat474 (e-PCR), detects polymorphism
- UniSTS:227256

AU048671 (e-PCR)
- UniSTS:145121

AA943436 (e-PCR)
- UniSTS:250108

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor 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 histone binding	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 transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within aortic smooth muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hematopoietic stem cell homeostasis	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell growth	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 negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology 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 spermatid development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of RSC-type complex	IEA Inferred from Electronic Annotation more info
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in intermediate filament cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in intermediate filament cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
part_of nBAF complex	ISO Inferred from Sequence Orthology more info
part_of npBAF complex	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: probable global transcription activator SNF2L2

Names: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2

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_001004446.2 → NP_001004446.2 probable global transcription activator SNF2L2 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

E9PTG1

Related

ENSRNOP00000016740.3, ENSRNOT00000016740.7
NM_001429133.1 → NP_001416062.1 probable global transcription activator SNF2L2 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

E9PTG1
NM_001429134.1 → NP_001416063.1 probable global transcription activator SNF2L2 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

E9PTG1
NM_001429135.1 → NP_001416064.1 probable global transcription activator SNF2L2 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I6ARN7

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_086019.1 Reference GRCr8

Range

233617277..233784908

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063268536.1 → XP_063124606.1 probable global transcription activator SNF2L2 isoform X2

Related

ENSRNOP00000080701.2, ENSRNOT00000110315.2
XM_063268547.1 → XP_063124617.1 probable global transcription activator SNF2L2 isoform X4
XM_063268552.1 → XP_063124622.1 probable global transcription activator SNF2L2 isoform X5

Related

ENSRNOP00000069210.2, ENSRNOT00000080124.3
XM_063268505.1 → XP_063124575.1 probable global transcription activator SNF2L2 isoform X1
XM_063268513.1 → XP_063124583.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268525.1 → XP_063124595.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268522.1 → XP_063124592.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268509.1 → XP_063124579.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268533.1 → XP_063124603.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268529.1 → XP_063124599.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268502.1 → XP_063124572.1 probable global transcription activator SNF2L2 isoform X1

Related

ENSRNOP00000095555.2, ENSRNOT00000095776.2
XM_063268527.1 → XP_063124597.1 probable global transcription activator SNF2L2 isoform X1

UniProtKB/TrEMBL

E9PTG1
XM_063268545.1 → XP_063124615.1 probable global transcription activator SNF2L2 isoform X3
XM_063268564.1 → XP_063124634.1 probable global transcription activator SNF2L2 isoform X6

Related

ENSRNOP00000089540.1, ENSRNOT00000116235.2
XM_063268556.1 → XP_063124626.1 probable global transcription activator SNF2L2 isoform X6

Related

ENSRNOP00000079036.2, ENSRNOT00000097032.2
XM_063268562.1 → XP_063124632.1 probable global transcription activator SNF2L2 isoform X6
XM_063268559.1 → XP_063124629.1 probable global transcription activator SNF2L2 isoform X6