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SMARCD1 Gene

protein-coding   GIFtS: 61
GCID: GC12P050478

SWI/SNF Related, Matrix Associated, Actin Dependent Regulator...

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of
Chromatin, Subfamily D, Member 11 2
     Chromatin Remodeling Complex BAF60A Subunit2
BAF60A2 3 5     Mammalian Chromatin Remodeling Complex BRG1-Associated Factor 60A2
60 KDa BRG-1/Brm-Associated Factor Subunit A2 3     SWI/SNF Complex 60 KDa Subunit A2
BRG1-Associated Factor 60A2 3     SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin
Subfamily D Member 12
CRACD12     Swp73-Like Protein2
Rsc6p2     SWI/SNF Complex 60 KDa Subunit3

External Ids:    HGNC: 111061   Entrez Gene: 66022   Ensembl: ENSG000000661177   OMIM: 6017355   UniProtKB: Q96GM53   

Export aliases for SMARCD1 gene to outside databases

Previous GC identifers: GC12P050773 GC12P050535 GC12P050195 GC12P048766 GC12P048767 GC12P048768 GC12P047511


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SMARCD1 Gene:
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)

GeneCards Summary for SMARCD1 Gene:
SMARCD1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1) is a protein-coding gene. Diseases associated with SMARCD1 include triple-a syndrome, and fanconi's anemia. GO annotations related to this gene include transcription coactivator activity and protein complex scaffold. An important paralog of this gene is SMARCD3.

UniProtKB/Swiss-Prot: SMRD1_HUMAN, Q96GM5
Function: Involved in chromatin remodeling. 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 (By similarity). Has a strong influence on
the 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.
Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for
transactivation. 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

Gene Wiki entry for SMARCD1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000012.12  NT_029419.13  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMARCD1 gene promoter:
         E2F-4   E2F-3a   STAT1   E2F-5   E2F-2   YY1   E2F-1   E2F   HSF2   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMARCD1 promoter sequence
   Search Chromatin IP Primers for SMARCD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMARCD1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q13-q14   Ensembl cytogenetic band:  12q13.12   HGNC cytogenetic band: 12q13-q14

SMARCD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMARCD1 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P050478:  view genomic region     (about GC identifiers)

Start:
50,478,755 bp from pter      End:
50,494,495 bp from pter
Size:
15,741 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMRD1_HUMAN, Q96GM5 (See protein sequence)
Recommended Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1  
Size: 515 amino acids; 58233 Da
Subunit: Component of the BAF 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. Specifically interacts with the VDR heterodimer complex. 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 ESR1, NR3C1, NR1H4, PGR, SMARCA4, SMARCC1 and SMARCC2.
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 (By similarity)
Sequence caution: Sequence=AAC50695.1; Type=Frameshift; Positions=30; Sequence=AAD23390.1; Type=Erroneous
initiation; Sequence=AAH09368.3; Type=Erroneous initiation;
Secondary accessions: A6NN27 Q92924 Q9Y635
Alternative splicing: 2 isoforms:  Q96GM5-1   Q96GM5-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SMARCD1: NX_Q96GM5

Explore proteomics data for SMARCD1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys101, Lys156, Lys223, Lys464
  • Modification sites at PhosphoSitePlus

  • See SMARCD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_003067.3  NP_620710.2  

    ENSEMBL proteins: 
     ENSP00000378414   ENSP00000370924   ENSP00000447386   ENSP00000448030   ENSP00000449825  
     ENSP00000448627   ENSP00000447909  

    SMARCD1 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR003121 SWIB_MDM2_domain
     IPR019835 SWIB_domain

    Graphical View of Domain Structure for InterPro Entry Q96GM5

    ProtoNet protein and cluster: Q96GM5

    1 Blocks protein domain: IPB003121 SWIB complex

    UniProtKB/Swiss-Prot: SMRD1_HUMAN, Q96GM5
    Similarity: Belongs to the SMARCD family
    Similarity: Contains 1 SWIB domain


    SMARCD1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SMRD1_HUMAN, Q96GM5
    Function: Involved in chromatin remodeling. 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 (By similarity). Has a strong influence on
    the 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.
    Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for
    transactivation. 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

         Genatlas biochemistry entry for SMARCD1:
    general transcriptional activator S cerevisiae SWI/SNF related protein,matrix associated,actin-dependent regulator
    of chromatin,subfamily D,member 1,component of the chromatin remodeling complex,ubiquitously expressed

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003713transcription coactivator activity NAS8804307
    GO:0005515protein binding IPI12917342
    GO:0032947protein complex scaffold IDA12917342
         
    SMARCD1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SMARCD1:
     Increased cell number in S 

    Animal Models:
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMARCD1

    miRNA
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    miRTarBase miRNAs that target SMARCD1:
    hsa-mir-7-5p (MIRT025886), hsa-mir-425-5p (MIRT039323), hsa-mir-101-3p (MIRT027347), hsa-mir-744-5p (MIRT037419), hsa-mir-223-3p (MIRT052651), hsa-let-7c-5p (MIRT051748), hsa-let-7b-5p (MIRT032437)

    Block miRNA regulation of human, mouse, rat SMARCD1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMARCD1 (see all 95):
    hsa-miR-1321 hsa-miR-631 hsa-miR-1914* hsa-miR-1224-3p hsa-miR-1260b hsa-miR-200a hsa-miR-4315 hsa-miR-877*
    SwitchGear 3'UTR luciferase reporter plasmidSMARCD1 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SMRD1_HUMAN, Q96GM5: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    endoplasmic reticulum1
    mitochondrion1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016514SWI/SNF complex IDA11078522
    GO:0071564npBAF complex ISS--
    GO:0071565nBAF complex ISS--

    SMARCD1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SMARCD1 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Transcription Ligand dependent activation of the ESR1 SP pathway
    Transcription Ligand dependent activation of the ESR1 SP pathway0.37
    Development Ligand dependent activation of the ESR1 AP 1 pathway0.37
    2AMPK Enzyme Complex Pathway
    Chromatin Remodeling0.00
    AMPK Enzyme Complex Pathway
    3PEDF Induced Signaling
    Glucocorticoid Receptor Signaling0.43
    4Prostate Cancer
    Prostate Cancer0.32
    5Glucocorticoid receptor regulatory network
    Glucocorticoid receptor regulatory network

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    4 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SMARCD1
        AMPK Enzyme Complex Pathway
    BRCA1 Pathway
    Glucocorticoid Receptor Signaling
    Chromatin Remodeling

    2 GeneGo (Thomson Reuters) Pathways for SMARCD1
        Transcription Ligand-dependent activation of the ESR1/SP pathway
    Development Ligand-dependent activation of the ESR1/AP-1 pathway

    2 BioSystems Pathways for SMARCD1
        Prostate Cancer
    Glucocorticoid receptor regulatory network


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMARCD1
    Interactions:

        GeneGlobe Interaction Network for SMARCD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SMARCD1 (Q96GM51, 2, 3 ENSP000003784144) via UniProtKB, MINT, STRING, and/or I2D (see all 970)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SMARCB1Q128242, 3, ENSP000002631214MINT-7945693 MINT-7947479 I2D: score=7 STRING: ENSP00000263121
    ARID1AO144972, 3, ENSP000003204854MINT-7945693 MINT-7947479 I2D: score=3 STRING: ENSP00000320485
    SMARCA4P515321, 3, ENSP000003507204EBI-358489,EBI-302489 I2D: score=9 STRING: ENSP00000350720
    KRT15P190122, 3, ENSP000002540434MINT-66111 I2D: score=5 STRING: ENSP00000254043
    LDOC1O957512, 3, ENSP000003595574MINT-67863 I2D: score=5 STRING: ENSP00000359557
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006337nucleosome disassembly IDA8895581
    GO:0006338chromatin remodeling IMP12917342
    GO:0006357regulation of transcription from RNA polymerase II promoter NAS8804307
    GO:0007399nervous system development IEA--
    GO:0048096chromatin-mediated maintenance of transcription IMP12917342

    SMARCD1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
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    Browse Tocris compounds for SMARCD1 (SMRD1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SMARCD1 gene (2 alternative transcripts): 
    NM_003076.4  NM_139071.2  

    Unigene Cluster for SMARCD1:

    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
    Hs.79335  [show with all ESTs]
    Unigene Representative Sequence: NM_003076
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000394963(uc001rvx.4 uc001rvy.4 uc009zlp.3) ENST00000381513
    ENST00000551966 ENST00000550477 ENST00000547247(uc010smo.1) ENST00000547637
    ENST00000551497 ENST00000548573 ENST00000549274 ENST00000550280 ENST00000551352
    ENST00000549526
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    Additional mRNA sequence: 

    AF109733.1 AK130517.1 AK292700.1 AK293932.1 BC000063.2 BC009368.2 U66617.1 

    15 DOTS entries:

    DT.86855136  DT.100685679  DT.100794327  DT.95310816  DT.100037423  DT.95147184  DT.121127795  DT.121127798 
    DT.100794328  DT.100794329  DT.100794331  DT.121127794  DT.95310765  DT.99941756  DT.121127817 

    Selected AceView cDNA sequences (see all 273):

    BE740488 BQ933801 BM740007 AA580866 BF821367 AL110449 BM543298 F09851 
    BQ218828 AI287806 BG056090 BQ010066 BX280691 BQ919072 BQ929257 BQ957208 
    CK430021 AU133315 BU160528 BU557139 BQ927245 AA835516 AA379818 BM470116 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SMARCD1 (see all 8)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b · 14c · 14d
    SP1:              -                                         -                                   -           -                                 
    SP2:              -                                         -                                   -     -     -                                 
    SP3:              -                             -     -     -                                                                                 
    SP4:              -                             -                                                                                             
    SP5:                                                                                                                                          


    ECgene alternative splicing isoforms for SMARCD1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SMARCD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACCAAACTT
    SMARCD1 Expression
    About this image


    SMARCD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
    SMARCD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMARCD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.79335

    UniProtKB/Swiss-Prot: SMRD1_HUMAN, Q96GM5
    Tissue specificity: Expressed in all tissues tested, including brain, heart, kidney, liver, lung, muscle, pancreas
    and placenta

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SMARCD1 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smarcd11 , 5 SWI/SNF related, matrix associated, actin dependent more1, 5 93.2(n)1
    99.42(a)1
      15 (56.13 cM)5
    837971  NM_031842.21  NP_114030.21 
     997022875 
    chicken
    (Gallus gallus)
    Aves SMARCD11 SWI/SNF related, matrix associated, actin dependent more 81.71(n)
    94.34(a)
      426882  XM_424488.4  XP_424488.3 
    lizard
    (Anolis carolinensis)
    Reptilia SMARCD16
    SWI/SNF related, matrix associated, actin dependen...
    96(a)
    1 ↔ 1
    2(91661768-91678770)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.54922 Xenopus laevis, similar to SWI/SNF related, clone IMAGE5542448, more 80.2(n)    BC045009.1 
    zebrafish
    (Danio rerio)
    Actinopterygii smarcd12 SWI/SNF related, matrix associated, actin dependent more 77.95(n)   323115  BC049347.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Bap601 , 3 general RNA polymerase II
    transcription factor3
    Brahma associated protein 60kD1
    78(a)3
    64.46(n)1
    71.58(a)1
      11E13
    322681  NM_078588.31  NP_511143.21 
    worm
    (Caenorhabditis elegans)
    Secernentea C18E3.23
    swsn-2.11
    swsn-2.11 53(a)
    (best of 2)3
    56.55(n)1
    58.42(a)1
      I(4210999-4212514)3
    1764261  NM_066849.41  NP_499250.11 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G018901 AT3G01890 48.78(n)
    38.48(a)
      820093  NM_111055.3  NP_566154.2 
    rice
    (Oryza sativa)
    Liliopsida Os04g03821001 Os04g0382100 50.42(n)
    39.62(a)
      4335638  NM_001059140.1  NP_001052605.1 


    ENSEMBL Gene Tree for SMARCD1 (if available)
    TreeFam Gene Tree for SMARCD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SMARCD1 gene
    SMARCD32  SMARCD22  
    2 SIMAP similar genes for SMARCD1 using alignment to 7 protein entries:     SMRD1_HUMAN (see all proteins):
    SMARCD3    SMARCD2

    SMARCD1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SMARCD1 (see all 357)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1840754111,2
    --50477972(+) CAGGCA/GCCCGC 2 -- us2k10--------
    rs2003597121,2
    C--50478147(+) TTAAT-/TTTAAA 2 -- us2k10--------
    rs2011287321,2
    --50478148(+) ATATT-/ATAAAA 2 -- us2k10--------
    rs26405331,2
    C--50478149(+) ATATTA/TAAAAA 2 -- us2k1 tfbs35Minor allele frequency- T:0.23NA WA EA 362
    rs1471897701,2
    --50478341(+) TACTTC/GGTAGG 2 -- us2k10--------
    rs108759961,2
    C,F--50478352(+) CTGAGG/TTGGGA 2 -- us2k17Minor allele frequency- T:0.29NA WA CSA 14
    rs48985461,2
    C,F,H--50478449(+) CATCTC/AAAAAA 2 -- us2k1 tfbs322Minor allele frequency- A:0.26NS EA NA WA CSA 2341
    rs765477241,2
    F--50478862(+) GTCCCC/TCTTTC 2 -- us2k11Minor allele frequency- T:0.04WA 118
    rs740900491,2
    C,F--50479498(+) TTACAC/TACCTG 2 -- int11Minor allele frequency- T:0.50WA 2
    rs780735021,2
    F--50479575(+) TACCTG/ATATGA 2 -- int13Minor allele frequency- A:0.08CSA WA 122

    HapMap Linkage Disequilibrium report for SMARCD1 (50478755 - 50494495 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SMARCD1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SMARCD1
    DNA2.0 Custom Variant and Variant Library Synthesis for SMARCD1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601735    OMIM disorders: --

    11 diseases for SMARCD1:    
    About MalaCards
    triple-a syndrome    fanconi's anemia    tonsillitis    hiv-1
    neuronitis    prostate cancer    thyroiditis    leukemia
    malaria    cerebritis    prostatitis

    1 disease from the University of Copenhagen DISEASES database for SMARCD1:
    triple-A syndrome

    SMARCD1 for disorders           About GeneDecksing


    Export disorders for SMARCD1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SMARCD1 gene, integrated from 10 sources (see all 57):
    (articles sorted by number of sources associating them with SMARCD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. (PubMed id 12917342)1, 2, 3, 9 Hsiao P.W.... Archer T.K. (Mol. Cell. Biol. 2003)
    2. Diversity and specialization of mammalian SWI/SNF complexes. (PubMed id 8804307)1, 2, 3 Wang W.... Crabtree G.R. (Genes Dev. 1996)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Five SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) genes are dispersed in the human genome. (PubMed id 9693044)1, 3 Ring H.Z....Francke U. (Genomics 1998)
    5. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. (PubMed id 8895581)1, 2 Wang W....Crabtree G.R. (EMBO J. 1996)
    6. Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. (PubMed id 24255178)1 Couzens A.L....Gingras A.C. (Sci Signal 2013)
    7. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (Nat. Methods 2013)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    9. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (Sci Signal 2012)
    10. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6602 HGNC: 11106 AceView: SMARCD1 Ensembl:ENSG00000066117 euGenes: HUgn6602
    ECgene: SMARCD1 H-InvDB: SMARCD1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SMARCD1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SMARCD1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SMARCD1 gene:
    Search GeneIP for patents involving SMARCD1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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