Mouse Gene Arid1a (ENSMUST00000008024.6) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Binds DNA non-specifically. Also involved in vitamin D- coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR- mediated transrepression of the CYP27B1 gene (By similarity). 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 post-mitotic 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 post-mitotic 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. (from UniProt A2BH40)
Gencode Transcript: ENSMUST00000008024.6
Gencode Gene: ENSMUSG00000007880.16
Transcript (Including UTRs)
   Position: mm10 chr4:133,679,941-133,756,769 Size: 76,829 Total Exon Count: 20 Strand: -
Coding Region
   Position: mm10 chr4:133,680,331-133,723,039 Size: 42,709 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:133,679,941-133,756,769)mRNA (may differ from genome)Protein (1902 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsMGIPubMed
ReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ARI1A_MOUSE
DESCRIPTION: RecName: Full=AT-rich interactive domain-containing protein 1A; Short=ARID domain-containing protein 1A; AltName: Full=BRG1-associated factor 250; Short=BAF250; AltName: Full=BRG1-associated factor 250a; Short=BAF250A; AltName: Full=Osa homolog 1; AltName: Full=SWI-like protein; AltName: Full=SWI/SNF complex protein p270; AltName: Full=SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1;
FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Binds DNA non-specifically. Also involved in vitamin D- coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR- mediated transrepression of the CYP27B1 gene (By similarity). 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 post-mitotic 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 post-mitotic 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.
SUBUNIT: Component of SWI/SNF chromatin remodeling complexes, in some of which it can be mutually exclusive with ARID1B/BAF250B. Component of the BAF (SWI/SNF-A) complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Component of the SWI/SNF-B (PBAF) complex, at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, perhaps SMARCD3/BAF60C, SMARCC1/BAF155, SMARCC2/BAF170, PB1/BAF180, ARID2/BAF200, ARID1A/BAF250A or ARID1B/BAF250B and actin. Component of the SWI/SNF Brm complex, at least composed of SMARCA2/BRM/BAF190B, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, BAF60 (one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C), SMARCC1/BAF155, SMARCC2/BAF170, ARID1A/BAF250A, SIN3A, HDAC1, HDAC2, and RBAP4. Component of the SWI/SNF complex Brg1(I), at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, BAF60 (one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C), SMARCC1/BAF155, SMARCC2/BAF170, ARID1A/BAF250A, SIN3A, and probably HDAC2 and RBAP4. Component of the SWI/SNF Brg1(II), at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, ARID1A/BAF250A and probably HDAC2 and RBAP4. Component of a SWI/SNF-like EPAFa complex, at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCC1/BAF155, SMARCC2/BAF170, BAF250A and MLLT1/ENL. Component of a SWI/SNF-like complex containing ARID1A/BAF250A and ARID1B/BAF250B. Interacts through its C- terminus with SMARCA2/BRM/BAF190B and SMARCA4/BRG1/BAF190A. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. Interacts with SMARCC1/BAF155 (By similarity). Component of neural progenitors- specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron- specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin.
INTERACTION: O35845:Smarca4; NbExp=2; IntAct=EBI-371499, EBI-371515;
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Widely expressed. Expressed at high levels in the testis.
DEVELOPMENTAL STAGE: Expressed ubiquitously throughout the developing spinal cord, brain and other embryonic tissues at E10.5-E16.5. In the earlier stages at E9.5 and E10.5, is fairly ubiquitous though with clearly elevated expression in the progress zone and lateral mesoderm of limb buds, optic and otic vesicle, neural tube, and brain. Later on at E11.5 and E12.5, expression becomes more restricted and is confined to the interdigital area of limbs, dorsal mes/metencephalon, neocortex, and neural tube. Expression is seen in the eye lens from E10.5 until E12.5.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR (By similarity).
SIMILARITY: Contains 1 ARID domain.

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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -149.10387-0.385 Picture PostScript Text
3' UTR -81.80390-0.210 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001606 - ARID/BRIGHT_DNA-bd
IPR011989 - ARM-like
IPR021906 - DUF3518

Pfam Domains:
PF01388 - ARID/BRIGHT DNA binding domain
PF12031 - Domain of unknown function (DUF3518)

SCOP Domains:
48371 - ARM repeat
46774 - ARID-like

ModBase Predicted Comparative 3D Structure on A2BH40
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0016922 ligand-dependent nuclear receptor binding
GO:0031491 nucleosome binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001704 formation of primary germ layer
GO:0001843 neural tube closure
GO:0003205 cardiac chamber development
GO:0003408 optic cup formation involved in camera-type eye development
GO:0006325 chromatin organization
GO:0006337 nucleosome disassembly
GO:0006338 chromatin remodeling
GO:0006344 maintenance of chromatin silencing
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007369 gastrulation
GO:0007399 nervous system development
GO:0007566 embryo implantation
GO:0019827 stem cell population maintenance
GO:0030520 intracellular estrogen receptor signaling pathway
GO:0030521 androgen receptor signaling pathway
GO:0030900 forebrain development
GO:0042921 glucocorticoid receptor signaling pathway
GO:0043044 ATP-dependent chromatin remodeling
GO:0045893 positive regulation of transcription, DNA-templated
GO:0055007 cardiac muscle cell differentiation
GO:0060674 placenta blood vessel development
GO:1901998 toxin transport

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016514 SWI/SNF complex
GO:0070603 SWI/SNF superfamily-type complex
GO:0071564 npBAF complex
GO:0071565 nBAF complex


-  Descriptions from all associated GenBank mRNAs
  AF268912 - Mus musculus Osa1 nuclear protein mRNA, complete cds.
BC082554 - Mus musculus AT rich interactive domain 1A (SWI-like), mRNA (cDNA clone MGC:96305 IMAGE:30622048), complete cds.
BC079591 - Mus musculus RIKEN cDNA 4121402D02 gene, mRNA (cDNA clone IMAGE:6406949), **** WARNING: chimeric clone ****.
AK142143 - Mus musculus 12 days embryo eyeball cDNA, RIKEN full-length enriched library, clone:D230050O08 product:AT rich interactive domain 1A (Swi1 like), full insert sequence.
BC028548 - Mus musculus AT rich interactive domain 1A (SWI-like), mRNA (cDNA clone IMAGE:5255796), complete cds.
AK048464 - Mus musculus 16 days embryo head cDNA, RIKEN full-length enriched library, clone:C130062P22 product:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1, full insert sequence.
AK171778 - Mus musculus activated spleen cDNA, RIKEN full-length enriched library, clone:F830010I07 product:unclassifiable, full insert sequence.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
m_hSWI-SNFpathway - Chromatin Remodeling by hSWI/SNF ATP-dependent Complexes
m_vdrPathway - Control of Gene Expression by Vitamin D Receptor

Reactome (by CSHL, EBI, and GO)

Protein A2BH40 (Reactome details) participates in the following event(s):

R-MMU-3215448 SWI/SNF chromatin remodelling complex enhances MEP50:PRMT5 methyltransferase activity
R-MMU-8938217 RUNX1 binds the SWI/SNF complex
R-MMU-3214858 RMTs methylate histone arginines
R-MMU-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-MMU-3247509 Chromatin modifying enzymes
R-MMU-8878171 Transcriptional regulation by RUNX1
R-MMU-4839726 Chromatin organization
R-MMU-212436 Generic Transcription Pathway
R-MMU-73857 RNA Polymerase II Transcription
R-MMU-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A2BH40, ARI1A_MOUSE, Baf250, Baf250a, BC082554, Osa1, Q640Q1, Q925Q1, Smarcf1, uc008vdj.1, uc008vdj.2
UCSC ID: uc008vdj.2
RefSeq Accession: NM_001363070
Protein: A2BH40 (aka ARI1A_MOUSE)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.