Tbio SMARCD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

Protein Summary

Description

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (PubMed:8804307, PubMed:29374058). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Has a strong influence on vitamin D-mediated transcriptional activity from an enhancer vitamin D receptor element (VDRE). May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor (VDR) heterodimer (PubMed:14698202). Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation (PubMed:12917342). The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• Q96GM5
• A6NN27
• Q92924
• Q9Y635

Gene Name

• SMARCD1

Ensembl ID

• ENST00000381513
• ENSP00000370924
• ENSG00000066117
• ENST00000394963
• ENSP00000378414

Symbol

• BAF60A
• Rsc6p
• BAF60A
• CRACD1

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
interacting protein	0.95
protein complex	0.85
transcription factor binding site profile	0.85
disease perturbation	0.79
histone modification site profile	0.79

Protein Classes

PANTHER Classes

Protein / Nucleic Acid Binding / Dna Binding Protein / Chromatin/chromatin-binding Protein / Swi/snf-related Matrix-associated Actin-dependent Regulator Of Chromatin Subfamily D Member 1

DTO Classes

Protein / Nucleic Acid Binding / Dna Binding Protein / Chromatin/chromatin-binding Protein / Swi/snf-related Matrix-associated Actin-dependent Regulator Of Chromatin Subfamily D Member 1

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 31.9   (req: < 5)

Gene RIFs: 7   (req: <= 3)

Antibodies: 250   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 31.9   (req: >= 5)

Gene RIFs: 7   (req: > 3)

Antibodies: 250   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 10

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

Find Targets by Sequence

Show Full Sequence

ProtVista Viewer

Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

Go To Tool

GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

Go To Tool

GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

Go To Tool

ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

Go To Tool

Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (147)

Explore Interacting Targets

1 – 10 of 147

• See Interactions on String-DB

SMARCC2

Tbio

Family:  TF; Epigenetic

Novelty:  0.02625321

p_int:  1

Score:  0.999

Data Source:  BioPlex,STRINGDB

DPF3

Tbio

Family:  Epigenetic

Novelty:  0.069151

p_int:  1

Score:  0.985

Data Source:  BioPlex,STRINGDB

DPF2

Tbio

Family:  Epigenetic

Novelty:  0.0403366

p_int:  1

Score:  0.945

Data Source:  BioPlex,STRINGDB

SMARCE1

Tbio

Family:  TF

Novelty:  0.01748089

p_int:  0.999999936

p_ni:  6.4e-8

Score:  0.997

Data Source:  BioPlex,STRINGDB

BCL7C

Tdark

Novelty:  0.31203802

p_int:  0.999999848

p_ni:  1.52e-7

Score:  0.898

Data Source:  BioPlex,STRINGDB

BICRA

Tbio

Novelty:  0.13482404

p_int:  0.999999785

p_ni:  2.14e-7

p_wrong:  2e-9

Score:  0.722

Data Source:  BioPlex,STRINGDB

BRD7

Tchem

Family:  Epigenetic

Novelty:  0.01820848

p_int:  0.999999697

p_ni:  3.03e-7

Score:  0.984

Data Source:  BioPlex,STRINGDB

BRD9

Tchem

Family:  Epigenetic

Novelty:  0.03450227

p_int:  0.999999579

p_ni:  4.2e-7

p_wrong:  1e-9

Score:  0.901

Data Source:  BioPlex,STRINGDB

DPF1

Tbio

Family:  Epigenetic

Novelty:  0.0713809

p_int:  0.999998801

p_ni:  0.000001195

p_wrong:  5e-9

Score:  0.979

Data Source:  BioPlex,STRINGDB

ARID1B

Tbio

Family:  TF

Novelty:  0.00731933

p_int:  0.999998691

p_ni:  0.000001308

p_wrong:  1e-9

Score:  0.998

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (14)

Reactome (8)

KEGG (2)

PathwayCommons (2)

WikiPathways (2)

Chromatin modifying enzymes (R-HSA-3247509)

Click on a row in the table to change the structure displayed.

Find Similar Targets

Items per page:

5

1 – 5 of 8

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Chromatin modifying enzymes	238 targets	R-HSA-3247509
Reactome	Chromatin organization	238 targets	R-HSA-4839726
Reactome	Gene expression (Transcription)	1452 targets	R-HSA-74160
Reactome	Generic Transcription Pathway	1195 targets	R-HSA-212436
Reactome	RMTs methylate histone arginines	49 targets	R-HSA-3214858

Name	Explore in Pharos	Explore in Source
Chromatin modifying enzymes	238 targets	R-HSA-3247509
Chromatin organization	238 targets	R-HSA-4839726
Gene expression (Transcription)	1452 targets	R-HSA-74160
Generic Transcription Pathway	1195 targets	R-HSA-212436
RMTs methylate histone arginines	49 targets	R-HSA-3214858

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (15)

Functions (4)

Components (5)

Processes (6)

Find Similar Targets

Items per page:

10

1 – 4 of 4

GO Term	Evidence	Assigned by
protein-containing complex scaffold activity	Inferred from Direct Assay (IDA)	UniProtKB
transcription coactivator activity	Non-traceable Author Statement (NAS)	BHF-UCL
chromatin binding	Inferred from Electronic Annotation (IEA)	Ensembl
signaling receptor binding	Inferred from Electronic Annotation (IEA)	Ensembl

Disease Associations (null)

No disease associations found

GWAS Traits (8)

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 8

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
myeloid white cell count	EFO_0007988	1	1	1		75.1
diastolic blood pressure	EFO_0006336	1	1	1		70.8
BMI-adjusted hip circumference	EFO_0008039	2	2	2		55.8
comparative body size at age 10, self-reported	EFO_0009819	1	1	1		50.6
hypertension	EFO_0000537	2	1	0	6.2	38.8

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 8

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
myeloid white cell count	EFO_0007988	1		75.1
diastolic blood pressure	EFO_0006336	1		70.8
BMI-adjusted hip circumference	EFO_0008039	2		55.8
comparative body size at age 10, self-reported	EFO_0009819	1		50.6
hypertension	EFO_0000537	0	6.2	38.8

Reset Zoom  Beta Count   Odds Ratio

Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
Acetylation
Alternative splicing
Chromatin regulator
Coiled coil
Complete proteome
Isopeptide bond
Methylation
Neurogenesis
Nucleus
Phosphoprotein

GWAS Trait Find Similar Targets

No Header	No Header
BMI-adjusted hip circumference
colorectal cancer
comparative body size at age 10, self-reported
diastolic blood pressure
hypertension
lymphocyte count
myeloid white cell count
schizophrenia

MGI Phenotype Find Similar Targets

No Header	No Header
digestive/alimentary phenotype
homeostasis/metabolism phenotype
liver/biliary system phenotype

IDG Resources

No IDG generated resources found

Orthologs (14)

1 – 5 of 14

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	VGNC:10373	451889
Macaque	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1		712130
Mouse	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	MGI:1933623	83797
Rat	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	RGD:1305406	363002
Dog	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	VGNC:46537	486548

Species	Name	OMA	EggNOG	Inparanoid
Chimp	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Macaque	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Mouse	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Rat	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Dog	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1

Publication Statistics

PubMed Score 31.90

PubMed score by year

Reset Zoom

PubTator Score 16.32

PubTator score by year

Reset Zoom

Related Publications

Text Mined References (34)

GeneRif Annotations (7)

Items per page:

10

0 of 0

PMID	Year	Title