smarca1 SNF2 related chromatin remodeling ATPase 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: smarca1provided by ZNC
Official Full Name: SNF2 related chromatin remodeling ATPase 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-070705-296
See related: Ensembl:ENSDARG00000012776 AllianceGenome:ZFIN:ZDB-GENE-070705-296
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: si:dkey-148b12.1
Summary: Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Acts upstream of or within neural plate anterior/posterior regionalization and primitive erythrocyte differentiation. Predicted to be located in chromatin. Predicted to be active in nucleus. Orthologous to human SMARCA1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 5

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (21852714..21888360, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (21348908..21384573, complement)

Chromosome 5 - NC_007116.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

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 ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation 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 chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase 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 nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neural plate anterior/posterior regionalization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within primitive erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within primitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: probable global transcription activator SNF2L1

Names: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1

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_001099997.1 → NP_001093467.1 probable global transcription activator SNF2L1

Status: PROVISIONAL

Source sequence(s)

CR848717, CU104724

UniProtKB/TrEMBL

A0A8M1NDM3, A5WUY4

Related

ENSDARP00000023313.8, ENSDART00000020725.10

Conserved Domains (7) summary

PLN03142
Location:54 → 1033

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd00046
Location:163 → 302

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:829 → 868

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 ...

pfam00271
Location:444 → 559

Helicase_C; Helicase conserved C-terminal domain

pfam09110
Location:728 → 811

HAND; HAND

pfam09111
Location:883 → 995

SLIDE; SLIDE

pfam13892
Location:44 → 70

DBINO; DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007116.7 Reference GRCz11 Primary Assembly

Range

21852714..21888360 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005165157.5 → XP_005165214.1 probable global transcription activator SNF2L1 isoform X1

UniProtKB/TrEMBL

A0A8M2BCD5

Conserved Domains (7) summary

PLN03142
Location:54 → 1012

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd00046
Location:163 → 302

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:808 → 847

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 ...

pfam00271
Location:444 → 559

Helicase_C; Helicase conserved C-terminal domain

pfam09110
Location:707 → 790

HAND; HAND

pfam09111
Location:862 → 974

SLIDE; SLIDE

pfam13892
Location:44 → 70

DBINO; DNA-binding domain