smarcc1a SWI/SNF related BAF chromatin remodeling complex subunit C1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: smarcc1aprovided by ZNC
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit C1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-080514-3
See related: Ensembl:ENSDARG00000017397 AllianceGenome:ZFIN:ZDB-GENE-080514-3
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: smarcc1
Summary: Predicted to enable histone binding activity. Acts upstream of or within definitive hemopoiesis and heart morphogenesis. Located in cytoplasm and nucleus. Is expressed in head; tail bud; and telencephalon. Human ortholog(s) of this gene implicated in hydrocephalus. Orthologous to human SMARCC1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 16

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (42423530..42461243, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (42519652..42557612, complement)

Chromosome 16 - NC_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Zebrafish smarcc1a mutants reveal requirements for BAF chromatin remodeling complexes in distinguishing the atrioventricular canal from the cardiac chambers.
Title: Zebrafish smarcc1a mutants reveal requirements for BAF chromatin remodeling complexes in distinguishing the atrioventricular canal from the cardiac chambers.
We demonstrate that through this interaction, BBS6 modulates the sub-cellular localization of SMARCC1 and find, by transcriptional profiling, similar transcriptional changes following smarcc1a and bbs6 manipulation. Our work identifies a new function for BBS6 in nuclear-cytoplasmic transport, and provides insight into the disease mechanism underlying the congenital heart defects in McKusick-Kaufman syndrome patients.
Title: Nuclear/cytoplasmic transport defects in BBS6 underlie congenital heart disease through perturbation of a chromatin remodeling protein.

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Pathways from PubChem

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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

G41844 (e-PCR)
- UniSTS:67127

z1215 (e-PCR), detects polymorphism
- UniSTS:205115

fb33h01.x1 (e-PCR)
- UniSTS:190416

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within definitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of nBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of npBAF complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: SWI/SNF complex subunit SMARCC1

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

NCBI Reference Sequences (RefSeq)

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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_007127.7 Reference GRCz11 Primary Assembly

Range

42423530..42461243 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005158282.5 → XP_005158339.1 SWI/SNF complex subunit SMARCC1 isoform X2

UniProtKB/TrEMBL

A0A8M2B4M4

Conserved Domains (5) summary

COG5259
Location:431 → 696

RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]

pfam04433
Location:439 → 524

SWIRM; SWIRM domain

pfam16495
Location:879 → 950

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:29 → 432

SWIRM-assoc_2; SWIRM-associated domain at the N-terminal

pfam16498
Location:692 → 752

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
XM_003200246.6 → XP_003200294.1 SWI/SNF complex subunit SMARCC1 isoform X1

UniProtKB/TrEMBL

A0A8M1RJ59, F1Q9K1

Related

ENSDARP00000103197.2, ENSDART00000109259.4

Conserved Domains (5) summary

COG5259
Location:439 → 704

RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]

pfam04433
Location:447 → 532

SWIRM; SWIRM domain

pfam16495
Location:887 → 958

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:29 → 440

SWIRM-assoc_2; SWIRM-associated domain at the N-terminal

pfam16498
Location:700 → 760

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal