Smarce1 SWI/SNF related BAF chromatin remodeling complex subunit E1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smarce1provided by RGD
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit E1provided by RGD
Primary source: RGD:1304726
See related: EnsemblRapid:ENSRNOG00000010676 AllianceGenome:RGD:1304726
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
Also known as: BAF57; RGD1304726
Summary: Predicted to enable N-acetyltransferase activity; RNA binding activity; and nuclear receptor binding activity. Involved in negative regulation of DNA-templated transcription and spermatid development. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 5; familial meningioma; and meningioma. Orthologous to human SMARCE1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 292.1), Lung (RPKM 237.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q31

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (84655468..84678259, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (84159270..84180547, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (87116827..87138890, complement)

Chromosome 10 - NC_086028.1 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?

The N terminus of Brdt is involved in the recognition of Smarce1 as well as in the reorganization of hyperacetylated round spermatid chromatin.
Title: Insights into role of bromodomain, testis-specific (Brdt) in acetylated histone H4-dependent chromatin remodeling in mammalian spermiogenesis.

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

RH138775 (e-PCR)
- UniSTS:220862

RH140914 (e-PCR)
- UniSTS:222928

RH137042 (e-PCR)
- UniSTS:219131

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables N-acetyltransferase activity	ISO Inferred from Sequence Orthology more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in neurogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in nucleosome disassembly	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 SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SWI/SNF complex	IEA Inferred from Electronic Annotation more info
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
part_of nBAF complex	IEA Inferred from Electronic Annotation more info
part_of nBAF complex	ISO Inferred from Sequence Orthology more info
part_of npBAF complex	IEA Inferred from Electronic Annotation more info
part_of npBAF complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation 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 E member 1

Names: BRG1-associated factor 57; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, 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_001024993.2 → NP_001020164.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform 2

See identical proteins and their annotated locations for NP_001020164.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

C0IMX4, C0IMX5, C0IMX6, Q56A18, Q5BJV2

UniProtKB/TrEMBL

E9PU44

Related

ENSRNOP00000014230.7, ENSRNOT00000014230.9

Conserved Domains (1) summary

cd01390
Location:35 → 96

HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...
NM_001399629.1 → NP_001386558.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6HIW9

Related

ENSRNOP00000074941.3, ENSRNOT00000083233.3

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_086028.1 Reference GRCr8

Range

84655468..84678259 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039086083.2 → XP_038942011.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X2

UniProtKB/TrEMBL

A6HIX0, E9PU44

Conserved Domains (2) summary

PTZ00121
Location:180 → 302

PTZ00121; MAEBL; Provisional

cd01390
Location:2 → 61

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
XM_039086085.2 → XP_038942013.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X1

UniProtKB/TrEMBL

E9PU44

Conserved Domains (2) summary

PTZ00121
Location:127 → 393

PTZ00121; MAEBL; Provisional

cd01390
Location:52 → 113

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
XM_039086082.2 → XP_038942010.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X2

UniProtKB/TrEMBL

A6HIX0, E9PU44

Conserved Domains (2) summary

PTZ00121
Location:180 → 302

PTZ00121; MAEBL; Provisional

cd01390
Location:2 → 61

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
XM_039086084.2 → XP_038942012.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X2

UniProtKB/TrEMBL

A6HIX0, E9PU44

Conserved Domains (2) summary

PTZ00121
Location:180 → 302

PTZ00121; MAEBL; Provisional

cd01390
Location:2 → 61

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...