Smarca5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarca5provided by MGI
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5provided by MGI
Primary source: MGI:MGI:1935129
See related: Ensembl:ENSMUSG00000031715 AllianceGenome:MGI:1935129
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Snf2h; MommeD4; 4933427E24Rik; D030040M08Rik; D330027N15Rik
Summary: Predicted to enable several functions, including ATP binding activity; ATP hydrolysis activity; and nucleosome array spacer activity. Predicted to contribute to histone binding activity. Involved in negative regulation of macromolecule biosynthetic process and positive regulation of DNA replication. Acts upstream of or within cellular response to leukemia inhibitory factor; chromatin organization; and positive regulation of DNA-templated transcription. Located in nucleus and pericentric heterochromatin. Part of NoRC complex and chromatin silencing complex. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Orthologous to human SMARCA5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 25.9), liver E14 (RPKM 13.9) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 8 C2; 8 38.41 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (81426572..81466088, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (80699943..80739459, complement)

Chromosome 8 - NC_000074.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

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.
E3 ubiquitin ligase RNF180 mediates the ALKBH5/SMARCA5 axis to promote colon inflammation and Th17/Treg imbalance in ulcerative colitis mice.
Title: E3 ubiquitin ligase RNF180 mediates the ALKBH5/SMARCA5 axis to promote colon inflammation and Th17/Treg imbalance in ulcerative colitis mice.
Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice.
Title: Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice.
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.
Chromatin Remodeling Enzyme Snf2h Is Essential for Retinal Cell Proliferation and Photoreceptor Maintenance.
Title: Chromatin Remodeling Enzyme Snf2h Is Essential for Retinal Cell Proliferation and Photoreceptor Maintenance.
Functional roles of the chromatin remodeler SMARCA5 in mouse and bovine preimplantation embryosdagger.
Title: Functional roles of the chromatin remodeler SMARCA5 in mouse and bovine preimplantation embryos†.
Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.
Title: Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.
these results indicate that Smarca5 plays a key role in the development of thymocytes undergoing beta-selection, gammadelta thymocytes, and also B cell progenitors by regulating the transcription of early differentiation programs
Title: ISWI ATPase Smarca5 Regulates Differentiation of Thymocytes Undergoing β-Selection.
demonstrate the importance of Snf2h in oocyte meiotic resumption, but also reveal the mechanism underlying how a chromatin remodeling factor can regulate oocyte meiosis
Title: The chromatin remodeler Snf2h is essential for oocyte meiotic cell cycle progression.
Smarca5 plays indispensable roles during early hematopoiesis and erythropoiesis.
Title: The ISWI ATPase Smarca5 (Snf2h) Is Required for Proliferation and Differentiation of Hematopoietic Stem and Progenitor Cells.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (3) 1 citation
Endonuclease-mediated (1)
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

H05L03.2 (e-PCR)
- UniSTS:311318

Smarca5 (e-PCR), detects polymorphism
- UniSTS:547368

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP-dependent chromatin remodeler activity	ISO Inferred from Sequence Orthology more info
enables ATP-dependent chromatin remodeler activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IEA Inferred from Electronic Annotation more info
contributes_to histone binding	ISO Inferred from Sequence Orthology more info
enables histone octamer slider activity	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA-templated transcription initiation	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription initiation	ISO Inferred from Sequence Orthology more info
involved_in antiviral innate immune response	IEA Inferred from Electronic Annotation more info
involved_in antiviral innate immune response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within chromatin organization	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within chromatin remodeling	IGI Inferred from Genetic Interaction 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
acts_upstream_of_or_within embryo development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of mitotic chromosome condensation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase I	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleosome assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA replication	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	TAS Traceable Author Statement 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	ISO Inferred from Sequence Orthology more info
involved_in rDNA heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA replication	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info

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

General protein information

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

Names: mSnf2h; sucrose nonfermenting protein 2 homolog

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_053124.2 → NP_444354.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

See identical proteins and their annotated locations for NP_444354.2

Status: PROVISIONAL

Source sequence(s)

BC053069

Consensus CDS

CCDS22442.1

UniProtKB/Swiss-Prot

Q8C791, Q8CA22, Q8VDG1, Q91ZW3, Q925M9

Related

ENSMUSP00000044361.9, ENSMUST00000043359.9

Conserved Domains (7) summary

smart00717
Location:841 → 882

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

cd00046
Location:199 → 338

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00167
Location:843 → 882

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

pfam00176
Location:182 → 462

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:481 → 596

Helicase_C; Helicase conserved C-terminal domain

pfam09110
Location:742 → 827

HAND; HAND

pfam09111
Location:897 → 1009

SLIDE; SLIDE