SMARCA5 SNF2 related chromatin remodeling ATPase 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCA5provided by HGNC
Official Full Name: SNF2 related chromatin remodeling ATPase 5provided by HGNC
Primary source: HGNC:HGNC:11101
See related: Ensembl:ENSG00000153147 MIM:603375; AllianceGenome:HGNC:11101
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: ISWI; SNF2H; hISWI; hSNF2H; WCRF135
Summary: The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 25.1), lung (RPKM 17.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q31.21

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (143513702..143557486)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (146830915..146874681)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (144434855..144478639)

Chromosome 4 - NC_000004.12 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis.
Title: SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis.
Circular RNA SMARCA5 Promotes a Poor Prognosis and Radiotherapy Resistance for Patients with Hepatocellular Carcinoma.
Title: Circular RNA SMARCA5 Promotes a Poor Prognosis and Radiotherapy Resistance for Patients with Hepatocellular Carcinoma.
Hyperglycemia-Suppressed SMARCA5 Disrupts Transcriptional Homeostasis to Facilitate Endothelial Dysfunction in Diabetes.
Title: Hyperglycemia-Suppressed SMARCA5 Disrupts Transcriptional Homeostasis to Facilitate Endothelial Dysfunction in Diabetes.
The RPA-RNF20-SNF2H cascade promotes proper chromosome segregation and homologous recombination repair.
Title: The RPA-RNF20-SNF2H cascade promotes proper chromosome segregation and homologous recombination repair.
Human SMARCA5 is continuously required to maintain nucleosome spacing.
Title: Human SMARCA5 is continuously required to maintain nucleosome spacing.
The miR-100-5p Targets SMARCA5 to Regulate the Apoptosis and Intracellular Survival of BCG in Infected THP-1 Cells.
Title: The miR-100-5p Targets SMARCA5 to Regulate the Apoptosis and Intracellular Survival of BCG in Infected THP-1 Cells.
Long noncoding RNA lncMREF promotes myogenic differentiation and muscle regeneration by interacting with the Smarca5/p300 complex.
Title: Long noncoding RNA lncMREF promotes myogenic differentiation and muscle regeneration by interacting with the Smarca5/p300 complex.
Circular RNA SMARCA5 functions as an anti-tumor candidate in colon cancer by sponging microRNA-552.
Title: Circular RNA SMARCA5 functions as an anti-tumor candidate in colon cancer by sponging microRNA-552.
Negative Correlation Between Circular RNA SMARC5 and MicroRNA 432, and Their Clinical Implications in Bladder Cancer Patients.
Title: Negative Correlation Between Circular RNA SMARC5 and MicroRNA 432, and Their Clinical Implications in Bladder Cancer Patients.
A circular RNA, circSMARCA5, inhibits prostate cancer proliferative, migrative, and invasive capabilities via the miR-181b-5p/miR-17-3p-TIMP3 axis.
Title: A circular RNA, circSMARCA5, inhibits prostate cancer proliferative, migrative, and invasive capabilities via the miR-181b-5p/miR-17-3p-TIMP3 axis.

Submit: New GeneRIF Correction See all GeneRIFs (57)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	The WICH complex, composed of WSTF and SNF2H, are identified to interact with HIV-1 Tat in Jurkat cell	PubMed
Vpr	vpr	HIV-1 Vpr directly binds SNF2H and the Vpr mutant lacking amino acids 71-75 abolishes its binding to SNF2H	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D4S846 (e-PCR)
- UniSTS:18775

MARC_12251-12252:1005143327:1 (e-PCR)
- UniSTS:267383

MARC_12251-12252:1008000416:1 (e-PCR)
- UniSTS:267383

RH122560 (e-PCR)
- UniSTS:138624

SHGC-67312 (e-PCR)
- UniSTS:90765

RH70242 (e-PCR)
- UniSTS:32200

SHGC-68114 (e-PCR)
- UniSTS:87505

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent chromatin remodeler activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent chromatin remodeler activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
contributes_to histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone octamer slider activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleosome array spacer activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleosome binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	NAS Non-traceable Author Statement more info	PubMed
involved_in DNA methylation-dependent constitutive heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA-templated transcription initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in antiviral innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mitotic chromosome condensation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of mitotic chromosome condensation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase I	ISO Inferred from Sequence Orthology more info
involved_in nucleosome assembly	EXP Inferred from Experiment more info	PubMed
involved_in nucleosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase I	NAS Non-traceable Author Statement more info	PubMed
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	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase III	IDA Inferred from Direct Assay more info	PubMed
involved_in rDNA heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of ACF complex	IPI Inferred from Physical Interaction more info	PubMed
part_of B-WICH complex	IDA Inferred from Direct Assay more info	PubMed
part_of CHRAC	NAS Non-traceable Author Statement more info	PubMed
part_of NURF complex	IDA Inferred from Direct Assay more info	PubMed
part_of NoRC complex	ISO Inferred from Sequence Orthology more info
part_of RSF complex	IPI Inferred from Physical Interaction more info	PubMed
part_of WICH complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of chromatin silencing complex	IEA Inferred from Electronic Annotation more info
located_in condensed chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in fibrillar center	IDA Inferred from Direct Assay more info
colocalizes_with nuclear replication fork	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement 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
located_in pericentric heterochromatin	EXP Inferred from Experiment more info	PubMed
located_in pericentric heterochromatin	ISO Inferred from Sequence Orthology more info
is_active_in site of double-strand break	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

Names: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin A5; sucrose nonfermenting protein 2 homolog; sucrose nonfermenting-like 5

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_003601.4 → NP_003592.3 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

See identical proteins and their annotated locations for NP_003592.3

Status: REVIEWED

Source sequence(s)

AC099396, AC104685, AC139713

Consensus CDS

CCDS3761.1

UniProtKB/Swiss-Prot

O60264

UniProtKB/TrEMBL

B4DZC0, B7ZAX9

Related

ENSP00000283131.3, ENST00000283131.4

Conserved Domains (1) summary

PLN03142
Location:69 → 1012

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional