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

Gene ID: 93762, updated on 10-Jun-2024

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 ATP-dependent activity, acting on DNA. Predicted to contribute to histone binding activity. Involved in rDNA heterochromatin assembly. Acts upstream of or within cellular response to leukemia inhibitory factor; chromatin organization; and positive regulation of transcription, DNA-templated. Located in nucleus. Part of ISWI-type 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, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 25.9), liver E14 (RPKM 13.9) and 27 other tissues See more
Orthologs
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Genomic context

See Smarca5 in Genome Data Viewer
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_000074.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 39209 Neighboring gene predicted gene, 46044 Neighboring gene Fras1 related extracellular matrix protein 3 Neighboring gene STARR-seq mESC enhancer starr_22039 Neighboring gene STARR-seq mESC enhancer starr_22040 Neighboring gene STARR-positive B cell enhancer ABC_E8847 Neighboring gene lactate dehydrogenase A pseudogene Neighboring gene growth factor receptor bound protein 2-associated protein 1 Neighboring gene predicted gene, 51580

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding ISO
Inferred from Sequence Orthology
more info
 
enables ATP hydrolysis activity ISO
Inferred from Sequence Orthology
more info
 
enables ATP-dependent activity, acting on DNA IBA
Inferred from Biological aspect of Ancestor
more info
 
enables ATP-dependent chromatin remodeler activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
 
contributes_to histone binding ISO
Inferred from Sequence Orthology
more info
 
enables histone octamer slider activity ISO
Inferred from Sequence Orthology
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables nucleosome binding IEA
Inferred from Electronic Annotation
more info
 
enables nucleotide 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 repair ISO
Inferred from Sequence Orthology
more info
 
involved_in DNA-templated transcription initiation 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 
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 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 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 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
 
part_of chromatin silencing complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in condensed chromosome ISO
Inferred from Sequence Orthology
more info
 
located_in fibrillar center ISO
Inferred from Sequence Orthology
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
 
part_of pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
part_of pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
 
is_active_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
 

General protein information

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)

  1. NM_053124.2NP_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:841882
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
    cd00046
    Location:199338
    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:843882
    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:182462
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:481596
    Helicase_C; Helicase conserved C-terminal domain
    pfam09110
    Location:742827
    HAND; HAND
    pfam09111
    Location:8971009
    SLIDE; SLIDE

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    81426572..81466088 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)