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    Smarca4 SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 171379, updated on 27-Nov-2024

    Summary

    Official Symbol
    Smarca4provided by RGD
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4provided by RGD
    Primary source
    RGD:621728
    See related
    EnsemblRapid:ENSRNOG00000009271 AllianceGenome:RGD:621728
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    brg-1
    Summary
    Enables chromatin binding activity. Involved in negative regulation of DNA-templated transcription; nucleosome disassembly; and spermatid development. Part of SWI/SNF complex. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid cancer. Orthologous to human SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 391.9), Adrenal (RPKM 353.5) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Smarca4 in Genome Data Viewer
    Location:
    8q13
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (28438370..28535071)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (20167717..20258975)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (22648323..22739468)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene coactivator-associated arginine methyltransferase 1 Neighboring gene Yip1 domain family, member 2 Neighboring gene translocase of inner mitochondrial membrane 29 Neighboring gene uncharacterized LOC134480145 Neighboring gene low density lipoprotein receptor Neighboring gene SPC24 component of NDC80 kinetochore complex

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables ATP-dependent activity, acting on DNA IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent activity, acting on DNA ISO
    Inferred from Sequence Orthology
    more info
     
    enables ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA polymerase binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA polymerase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase I core promoter sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    contributes_to RNA polymerase I core promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables Tat protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables Tat protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables lncRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nuclear androgen receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclear androgen receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nucleosome array spacer activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables p53 binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables p53 binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription coregulator binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription corepressor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription corepressor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in RNA polymerase I preinitiation complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within aorta development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within aortic smooth muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within blastocyst growth ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within blastocyst hatching ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within blood vessel development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cell morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within coronary vasculature development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within definitive erythrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within embryonic hindlimb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within embryonic organ morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within epidermis morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within forebrain development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within_negative_effect gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within glial cell fate determination ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within heart development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within heart trabecula formation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within hindbrain development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within in utero embryonic development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within keratinocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within lens fiber cell development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within liver development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of androgen receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of androgen receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nervous system development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neural retina development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural retina development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neurogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nucleosome disassembly IDA
    Inferred from Direct Assay
    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
     
    acts_upstream_of_or_within outflow tract morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within pharyngeal arch artery morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation by host of viral transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation by host of viral transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cold-induced thermogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of glucose mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of glucose mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of miRNA transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of miRNA transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within primitive erythrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in spermatid development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in transcription initiation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within vasculogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within ventricular septum development ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of SWI/SNF complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in euchromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
     
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
     
    located_in male germ cell nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of nBAF complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of npBAF complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of npBAF complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of npBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    transcription activator BRG1
    Names
    ATP-dependent helicase SMARCA4
    BAF190A
    BRG1-associated factor 190A
    SNF2-beta
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
    protein brahma homolog 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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)

    1. NM_134368.1NP_599195.1  transcription activator BRG1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      Q8K1P7
      Related
      ENSRNOP00000081001.1, ENSRNOT00000097065.2
      Conserved Domains (9) summary
      cd05516
      Location:14251530
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:612656
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:460532
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:774913
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:43164
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:7571052
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10791194
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:171205
      QLQ; QLQ
      pfam14619
      Location:12891356
      SnAC; Snf2-ATP coupling, chromatin remodelling complex

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      28438370..28535071
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006242598.4XP_006242660.1  transcription activator BRG1 isoform X3

      See identical proteins and their annotated locations for XP_006242660.1

      UniProtKB/Swiss-Prot
      Q8K1P7
      UniProtKB/TrEMBL
      A6JNT8, G3V790
      Related
      ENSRNOP00000013166.7, ENSRNOT00000013165.8
      Conserved Domains (9) summary
      cd05516
      Location:14581564
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00573
      Location:460532
      HSA; domain in helicases and associated with SANT domains
      PLN03142
      Location:7501232
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      COG1196
      Location:370570
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam09606
      Location:42217
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      cd18062
      Location:731981
      DEXHc_SMARCA4; DEXH-box helicase domain of SMARCA4
      pfam07533
      Location:612654
      BRK; BRK domain
      pfam08880
      Location:171205
      QLQ
      pfam14619
      Location:13231389
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
    2. XM_006242599.4XP_006242661.1  transcription activator BRG1 isoform X4

      UniProtKB/Swiss-Prot
      Q8K1P7
      Conserved Domains (9) summary
      cd05516
      Location:14581563
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:612656
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:460532
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:774913
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:43164
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:7571052
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10791194
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:171205
      QLQ; QLQ
      pfam14619
      Location:13221389
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
    3. XM_063264830.1XP_063120900.1  transcription activator BRG1 isoform X1

    4. XM_063264832.1XP_063120902.1  transcription activator BRG1 isoform X2

    5. XM_006242601.4XP_006242663.1  transcription activator BRG1 isoform X7

      See identical proteins and their annotated locations for XP_006242663.1

      UniProtKB/Swiss-Prot
      Q8K1P7
      UniProtKB/TrEMBL
      A6JNT9
      Related
      ENSRNOP00000107457.1, ENSRNOT00000140415.1
      Conserved Domains (9) summary
      cd05516
      Location:14251531
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:612656
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:460532
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:774913
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:43164
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:7571052
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10791194
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:171205
      QLQ; QLQ
      pfam14619
      Location:12891356
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
    6. XM_063264833.1XP_063120903.1  transcription activator BRG1 isoform X5

    7. XM_063264834.1XP_063120904.1  transcription activator BRG1 isoform X6

    8. XM_063264835.1XP_063120905.1  transcription activator BRG1 isoform X1

    9. XM_063264836.1XP_063120906.1  transcription activator BRG1 isoform X1

    10. XM_063264831.1XP_063120901.1  transcription activator BRG1 isoform X1