Smarca5 SNF2 related chromatin remodeling ATPase 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smarca5provided by RGD
Official Full Name: SNF2 related chromatin remodeling ATPase 5provided by RGD
Primary source: RGD:1308832
See related: EnsemblRapid:ENSRNOG00000018149 AllianceGenome:RGD:1308832
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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. Predicted to be involved in several processes, including antiviral innate immune response; chromatin remodeling; and regulation of DNA-templated transcription. Predicted to act upstream of or within cellular response to leukemia inhibitory factor; chromatin remodeling; and positive regulation of DNA-templated transcription. Predicted to be located in chromosome and nuclear lumen. Predicted to be part of nucleus. Predicted to be active in nucleus and site of double-strand break. Orthologous to human SMARCA5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 348.6), Spleen (RPKM 260.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19q11

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (44172465..44208967)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (27271918..27304594)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (30936703..30969454)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: 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?

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General gene information

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Gene Ontology Provided by RGD

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 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 chromatin binding	IBA Inferred from Biological aspect of Ancestor 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 nucleosome array spacer activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleosome binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA-templated transcription initiation	ISO Inferred from Sequence Orthology more info
involved_in antiviral innate immune response	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin organization	ISO Inferred from Sequence Orthology more info
involved_in chromatin organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase I	ISO Inferred from Sequence Orthology more info
involved_in nucleosome assembly	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
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 III	ISO Inferred from Sequence Orthology more info
involved_in rDNA heterochromatin formation	ISO Inferred from Sequence Orthology more info
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 ISWI-type complex	ISO Inferred from Sequence Orthology more info
part_of NURF complex	ISO Inferred from Sequence Orthology more info
part_of NoRC complex	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in nuclear replication fork	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
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

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

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_001107419.1 → NP_001100889.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

See identical proteins and their annotated locations for NP_001100889.1

Status: PROVISIONAL

Source sequence(s)

CH473972

UniProtKB/TrEMBL

A6IYH1, F1LNL2

Related

ENSRNOP00000080637.1, ENSRNOT00000095459.2

Conserved Domains (7) summary

smart00717
Location:785 → 826

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

cd00046
Location:143 → 282

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:787 → 826

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:126 → 406

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:425 → 540

Helicase_C; Helicase conserved C-terminal domain

pfam09110
Location:686 → 771

HAND; HAND

pfam09111
Location:841 → 953

SLIDE; SLIDE

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_086037.1 Reference GRCr8

Range

44172465..44208967

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063278020.1 → XP_063134090.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 isoform X1

UniProtKB/TrEMBL

F1LNL2
XM_063278021.1 → XP_063134091.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 isoform X2