Smarcc2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarcc2provided by MGI
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2provided by MGI
Primary source: MGI:MGI:1915344
See related: Ensembl:ENSMUSG00000025369 AllianceGenome:MGI:1915344
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 5930405J04Rik
Summary: Enables chromatin binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Part of SWI/SNF complex; nBAF complex; and npBAF complex. Is expressed in cranial ganglion; genitourinary system; and inner ear. Orthologous to human SMARCC2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E14 (RPKM 85.9), whole brain E14.5 (RPKM 78.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10; 10 D3

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (128294823..128326460)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (128459182..128490591)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170.
Title: SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170.
These findings demonstrate involvement of BAF170-dependent chromatin remodeling in hippocampal neurogenesis.
Title: Ablation of BAF170 in Developing and Postnatal Dentate Gyrus Affects Neural Stem Cell Proliferation, Differentiation, and Learning.
BAF170 mediates the interaction between BAF complexes and H3K27demethylases, controlling the global level of H3K27me2/3 and ultimately the gene expression program in cortical development.
Title: Loss of BAF (mSWI/SNF) Complexes Causes Global Transcriptional and Chromatin State Changes in Forebrain Development.
Data show that knockdown of component of chromatin remodeling complex Brm or Baf170 at different stages promotes reprogramming.
Title: Knockdown of Brm and Baf170, Components of Chromatin Remodeling Complex, Facilitates Reprogramming of Somatic Cells.
BAF170 acts within a precise time window to repress indirect cortical neurogenesis, and control cortical size.
Title: Chromatin regulation by BAF170 controls cerebral cortical size and thickness.

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Variation

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Alleles

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

Targeted (4) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the Smarcc2 gene: The Smarcc2 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, zebrafish, fruit fly, mosquito, and frog.
Orthologs from Annotation Pipeline: 444 organisms have orthologs with human gene Smarcc2
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
involved_in nucleosome disassembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of double-strand break repair	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of myoblast differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of G0 to G1 transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of G1/S transition of mitotic cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of mitotic metaphase/anaphase transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of nucleotide-excision repair	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of RSC-type complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
part_of SWI/SNF complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF superfamily-type complex	IDA Inferred from Direct Assay more info	PubMed
part_of bBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of brahma complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	NAS Non-traceable Author Statement more info	PubMed
located_in kinetochore	NAS Non-traceable Author Statement more info	PubMed
part_of nBAF complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of nBAF complex	IDA Inferred from Direct Assay more info	PubMed
part_of nBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of npBAF complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of npBAF complex	IDA Inferred from Direct Assay more info	PubMed
part_of npBAF complex	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: SWI/SNF complex subunit SMARCC2

Names: BAF170; BRG1-associated factor 170; SWI/SNF complex 170 kDa subunit; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2

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_001114096.1 → NP_001107568.1 SWI/SNF complex subunit SMARCC2 isoform 2

See identical proteins and their annotated locations for NP_001107568.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an additional in-frame exon in the central coding region and lacks an in-frame segment in the 3' coding region, compared to variant 1. The resulting isoform (2) is shorter and has an additional segment in the central region but lacks an internal segment in the C-terminal region, compared to isoform 1.

Source sequence(s)

AI463326, AK146971, BC058720, CB248220

Consensus CDS

CCDS48726.1

UniProtKB/Swiss-Prot

Q6PDG5

UniProtKB/TrEMBL

A0A6P5QJP5, Q3UID0

Related

ENSMUSP00000096734.4, ENSMUST00000099131.11

Conserved Domains (5) summary

COG5259
Location:379 → 739

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

pfam16495
Location:911 → 977

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:715 → 779

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

cl30717
Location:719 → 874

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]
NM_001114097.1 → NP_001107569.1 SWI/SNF complex subunit SMARCC2 isoform 1

See identical proteins and their annotated locations for NP_001107569.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AI463326, BC058720, BC062102, CB248220

Consensus CDS

CCDS48727.1

UniProtKB/Swiss-Prot

Q6P6P3, Q6PDG5

UniProtKB/TrEMBL

A0A6P5QD21

Related

ENSMUSP00000100868.3, ENSMUST00000105235.10

Conserved Domains (6) summary

PTZ00121
Location:690 → 926

PTZ00121; MAEBL; Provisional

PHA03247
Location:963 → 1202

PHA03247; large tegument protein UL36; Provisional

COG5259
Location:379 → 708

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

pfam16495
Location:880 → 946

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:684 → 748

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
NM_001372395.1 → NP_001359324.1 SWI/SNF complex subunit SMARCC2 isoform 4

Status: VALIDATED

Source sequence(s)

AC170752

UniProtKB/TrEMBL

A0A6P5QJV1

Conserved Domains (6) summary

PTZ00121
Location:721 → 957

PTZ00121; MAEBL; Provisional

PHA03247
Location:994 → 1233

PHA03247; large tegument protein UL36; Provisional

COG5259
Location:379 → 739

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

pfam16495
Location:911 → 977

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:715 → 779

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
NM_198160.2 → NP_937803.1 SWI/SNF complex subunit SMARCC2 isoform 3

See identical proteins and their annotated locations for NP_937803.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, compared to variant 1. The resulting isoform (3) is shorter and lacks an internal segment in the C-terminal region, compared to isoform 1.

Source sequence(s)

AI463326, BC058720, CB248220

Consensus CDS

CCDS24278.1

UniProtKB/Swiss-Prot

Q6PDG5

UniProtKB/TrEMBL

A0A6P5QLK2

Related

ENSMUSP00000026433.8, ENSMUST00000026433.9

Conserved Domains (5) summary

COG5259
Location:379 → 708

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

pfam16495
Location:880 → 946

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:684 → 748

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

cl30717
Location:688 → 843

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000076.7 Reference GRCm39 C57BL/6J

Range

128294823..128326460

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006514023.5 → XP_006514086.1 SWI/SNF complex subunit SMARCC2 isoform X3

Conserved Domains (5) summary

COG5259
Location:379 → 739

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

pfam16495
Location:911 → 977

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:715 → 779

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

cl30717
Location:719 → 874

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]
XM_006514021.5 → XP_006514084.1 SWI/SNF complex subunit SMARCC2 isoform X1

UniProtKB/TrEMBL

A0A6P7RR74

Conserved Domains (6) summary

PTZ00121
Location:720 → 956

PTZ00121; MAEBL; Provisional

PHA03247
Location:993 → 1232

PHA03247; large tegument protein UL36; Provisional

COG5259
Location:379 → 738

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

pfam16495
Location:910 → 976

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:714 → 778

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
XM_006514024.5 → XP_006514087.1 SWI/SNF complex subunit SMARCC2 isoform X4

Conserved Domains (5) summary

COG5259
Location:379 → 738

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

pfam16495
Location:910 → 976

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:714 → 778

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

cl30717
Location:718 → 873

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]
XM_036155968.1 → XP_036011861.1 SWI/SNF complex subunit SMARCC2 isoform X5

Conserved Domains (5) summary

COG5259
Location:379 → 738

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

cl30717
Location:718 → 873

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

pfam16495
Location:910 → 976

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:714 → 778

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
XM_036155969.1 → XP_036011862.1 SWI/SNF complex subunit SMARCC2 isoform X6

Conserved Domains (5) summary

COG5259
Location:379 → 708

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

cl30717
Location:688 → 843

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

pfam16495
Location:880 → 946

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:684 → 748

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
XM_006514022.5 → XP_006514085.1 SWI/SNF complex subunit SMARCC2 isoform X2

UniProtKB/TrEMBL

A0A6P5QQX7

Conserved Domains (6) summary

PTZ00121
Location:689 → 925

PTZ00121; MAEBL; Provisional

PHA03247
Location:962 → 1201

PHA03247; large tegument protein UL36; Provisional

COG5259
Location:379 → 707

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

pfam16495
Location:879 → 945

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:683 → 747

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
XM_036155970.1 → XP_036011863.1 SWI/SNF complex subunit SMARCC2 isoform X7

Conserved Domains (5) summary

COG5259
Location:379 → 707

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

cl30717
Location:687 → 842

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

pfam16495
Location:879 → 945

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:683 → 747

SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
XM_030245245.2 → XP_030101105.1 SWI/SNF complex subunit SMARCC2 isoform X8

Conserved Domains (5) summary

COG5259
Location:379 → 707

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

pfam16495
Location:879 → 945

SWIRM-assoc_1; SWIRM-associated region 1

pfam16496
Location:7 → 420

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

pfam16498
Location:683 → 747

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

cl30717
Location:687 → 842

InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]