SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCE1provided by HGNC
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1provided by HGNC
Primary source: HGNC:HGNC:11109
See related: Ensembl:ENSG00000073584 MIM:603111; AllianceGenome:HGNC:11109
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CSS5; BAF57
Summary: The protein encoded by this gene is part of the large ATP-dependent chromatin remodeling complex SWI/SNF, which is required for transcriptional activation of genes normally repressed by chromatin. The encoded protein, either alone or when in the SWI/SNF complex, can bind to 4-way junction DNA, which is thought to mimic the topology of DNA as it enters or exits the nucleosome. The protein contains a DNA-binding HMG domain, but disruption of this domain does not abolish the DNA-binding or nucleosome-displacement activities of the SWI/SNF complex. Unlike most of the SWI/SNF complex proteins, this protein has no yeast counterpart. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in endometrium (RPKM 61.3), ovary (RPKM 41.8) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 17q21.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (40624962..40647818, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (41489340..41512196, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (38781214..38804070, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SMARCE1 promotes neuroblastoma tumorigenesis through assisting MYCN-mediated transcriptional activation.
Title: SMARCE1 promotes neuroblastoma tumorigenesis through assisting MYCN-mediated transcriptional activation.
Assembly and interaction of core subunits of BAF complexes and crystal study of the SMARCC1/SMARCE1 binary complex.
Title: Assembly and interaction of core subunits of BAF complexes and crystal study of the SMARCC1/SMARCE1 binary complex.
BAF57 Is a Potential Determinant of Colorectal Cancer Malignancy.
Title: BAF57 Is a Potential Determinant of Colorectal Cancer Malignancy.
Clear cell meningiomas are defined by a highly distinct DNA methylation profile and mutations in SMARCE1.
Title: Clear cell meningiomas are defined by a highly distinct DNA methylation profile and mutations in SMARCE1.
Long noncoding RNA HOTTIP promotes the metastatic potential of ovarian cancer through the regulation of the miR-615-3p/SMARCE1 pathway.
Title: Long noncoding RNA HOTTIP promotes the metastatic potential of ovarian cancer through the regulation of the miR-615-3p/SMARCE1 pathway.
BAF57/SMARCE1 Interacting with Splicing Factor SRSF1 Regulates Mechanical Stress-Induced Alternative Splicing of Cyclin D1.
Title: BAF57/SMARCE1 Interacting with Splicing Factor SRSF1 Regulates Mechanical Stress-Induced Alternative Splicing of Cyclin D1.
The importance of genetic counseling and screening for people with pathogenic SMARCE1 variants: A family study.
Title: The importance of genetic counseling and screening for people with pathogenic SMARCE1 variants: A family study.
Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA.
Title: Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA.
MicroRNA-802 induces hepatitis B virus replication and replication through regulating SMARCE1 expression in hepatocellular carcinoma.
Title: MicroRNA-802 induces hepatitis B virus replication and replication through regulating SMARCE1 expression in hepatocellular carcinoma.
A de novo splicing mutation in SMARCE1 was identified in a patient with Angelman-like syndrome.
Title: Identification of a de novo splicing variant in the Coffin-Siris gene, SMARCE1, in a patient with Angelman-like syndrome.

Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Coffin-Siris syndrome 5 MedGen: C4310788 OMIM: 616938 GeneReviews: Not available	Compare labs
Familial meningioma MedGen: C3551915 OMIM: 607174 GeneReviews: MN1 C-Terminal Truncation Syndrome	Compare labs

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

STS-AA035420 (e-PCR)
- UniSTS:22083

A002R45 (e-PCR)
- UniSTS:27721

D17S1237 (e-PCR)
- UniSTS:149850

SMARCE1_2145 (e-PCR)
- UniSTS:281023

RH103157 (e-PCR)
- UniSTS:97491

Homology

Homologs of the SMARCE1 gene: The SMARCE1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 395 organisms have orthologs with human gene SMARCE1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables N-acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	TAS Traceable Author Statement more info	PubMed
enables nuclear receptor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables nuclear receptor binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	HDA more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in neurogenesis	IEA Inferred from Electronic Annotation more info
involved_in nucleosome disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation 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 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 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	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of RSC-type complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
part_of SWI/SNF complex	NAS Non-traceable Author Statement more info	PubMed
part_of bBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of brahma complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	HDA more info	PubMed
located_in chromatin	NAS Non-traceable Author Statement more info	PubMed
located_in kinetochore	NAS Non-traceable Author Statement more info	PubMed
part_of nBAF complex	ISS Inferred from Sequence or Structural Similarity more info
part_of nBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of npBAF complex	ISS Inferred from Sequence or Structural Similarity more info
part_of npBAF complex	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear chromosome	TAS Traceable Author Statement more info	PubMed
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info
part_of protein-containing complex	HDA more info	PubMed

General protein information

Go to the top of the page Help

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 e1; chromatin remodeling complex BRG1-associated factor 57

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Genomic

NG_032163.1 RefSeqGene

Range

5001..25132

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003079.5 → NP_003070.3 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

See identical proteins and their annotated locations for NP_003070.3

Status: REVIEWED

Source sequence(s)

AC004585, AK095047, BC063700, BQ707908

Consensus CDS

CCDS11370.1

UniProtKB/Swiss-Prot

O43539, Q969G3

UniProtKB/TrEMBL

A0A024R1S7

Related

ENSP00000323967.6, ENST00000348513.12

Conserved Domains (3) summary

PTZ00121
Location:110 → 411

PTZ00121; MAEBL; Provisional

COG3883
Location:227 → 320

CwlO1; Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO [Function unknown]

cd01390
Location:70 → 131

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 ...