Smarcd2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarcd2provided by MGI
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2provided by MGI
Primary source: MGI:MGI:1933621
See related: Ensembl:ENSMUSG00000078619 AllianceGenome:MGI:1933621
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: Baf60b
Summary: Predicted to enable transcription coregulator activity. Predicted to be involved in nucleosome disassembly and regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and sensory organ. Orthologous to human SMARCD2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in thymus adult (RPKM 97.9), adrenal adult (RPKM 42.3) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 E1; 11 68.89 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (106153997..106163810, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (106263171..106272998, complement)

Chromosome 11 - NC_000077.7 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: Mouse ENCODE transcriptome data 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?

Baf60b, a member of the SWI/SNF chromatin remodeling complex, links chromatin opening to ATM activation by facilitating ATM recruitment to the open chromatin regions of a panel of hepatic gene loci.
Title: Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening.
the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia, was investigated.
Title: SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance.
the Rac- and Unkempt-dependent process leading to BAF60b ubiquitination takes place in the nuclear compartment
Title: The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (1)
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

M60510 (e-PCR)
- UniSTS:124962

AW322457 (e-PCR)
- UniSTS:185921

MARC_26036-26037:1032447192:1 (e-PCR)
- UniSTS:268920

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
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 nucleosome disassembly	IEA Inferred from Electronic Annotation more info
involved_in nucleosome disassembly	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
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement 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
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
located_in nuclear matrix	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

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2

Names: 60 kDa BRG-1/Brm-associated factor subunit B; BRG1-associated factor 60B

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_001130187.1 → NP_001123659.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 1

See identical proteins and their annotated locations for NP_001123659.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK159259, BB642181, BE853586, DV648475

Consensus CDS

CCDS48958.1

UniProtKB/Swiss-Prot

B1ARI7, B1ARJ6, Q99JR8

UniProtKB/TrEMBL

Q3TXH6

Related

ENSMUSP00000021052.10, ENSMUST00000021052.16

Conserved Domains (2) summary

COG5531
Location:230 → 425

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

pfam02201
Location:310 → 381

SWIB; SWIB/MDM2 domain
NM_031878.2 → NP_114084.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK159259, BE853586, CO425905, DV648475

Consensus CDS

CCDS48957.1

UniProtKB/TrEMBL

Q3TXH6

Related

ENSMUSP00000102456.2, ENSMUST00000106843.8

Conserved Domains (2) summary

COG5531
Location:183 → 378

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

pfam02201
Location:263 → 334

SWIB; SWIB/MDM2 domain

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

NC_000077.7 Reference GRCm39 C57BL/6J

Range

106153997..106163810 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006534552.5 → XP_006534615.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform X1

UniProtKB/TrEMBL

Q3TXH6

Conserved Domains (3) summary

TIGR01628
Location:43 → 161

PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

COG5531
Location:250 → 445

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

cd17675
Location:327 → 406

SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins