Human Gene SMARCD2 (uc010deb.1) Description and Page Index
  Description: Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 (SMARCD2), mRNA.
RefSeq Summary (NM_001098426): 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR7346977.1175383.1, SRR1163655.53614.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:61,909,441-61,920,351 Size: 10,911 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr17:61,910,298-61,920,034 Size: 9,737 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:61,909,441-61,920,351)mRNA (may differ from genome)Protein (531 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SMRD2_HUMAN
DESCRIPTION: RecName: Full=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2; AltName: Full=60 kDa BRG-1/Brm-associated factor subunit B; AltName: Full=BRG1-associated factor 60B; Short=BAF60B;
FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).
SUBUNIT: Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1, 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. May interact with SMARCA4, the catalytic subunit of the SWI/SNF related nucleosome- remodeling complexes BRG1(I) and BRG1(II). The precise distribution of the related SMARCD1, SMARCD2 and SMARCD3 proteins among these and other SWI/SNF nucleosome-remodeling complexes is not fully known. Interacts with UNKL.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Isoform 2 is expressed in the pancreas.
PTM: Ubiquitinated through a signaling process involving RAC1 and the RING finger protein UNKL.
SIMILARITY: Belongs to the SMARCD family.
SIMILARITY: Contains 1 SWIB domain.
SEQUENCE CAUTION: Sequence=AAC50696.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAF20280.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  MalaCards Disease Associations
  MalaCards Gene Search: SMARCD2
Diseases sorted by gene-association score: specific granule deficiency 2* (900), specific granule deficiency* (283), neutrophil-specific granule deficiency* (283)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 59.54 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 1465.20 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -145.00317-0.457 Picture PostScript Text
3' UTR -360.39857-0.421 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
IPR003121 - SWIB_MDM2_domain

Pfam Domains:
PF02201 - SWIB/MDM2 domain

SCOP Domains:
47592 - SWIB/MDM2 domain

ModBase Predicted Comparative 3D Structure on Q92925
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0006325 chromatin organization
GO:0006337 nucleosome disassembly
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0043044 ATP-dependent chromatin remodeling

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016514 SWI/SNF complex
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  LF209398 - JP 2014500723-A/16901: Polycomb-Associated Non-Coding RNAs.
AK025917 - Homo sapiens cDNA: FLJ22264 fis, clone HRC03066, highly similar to AF113019 Homo sapiens PRO2451 mRNA.
BC018953 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2, mRNA (cDNA clone IMAGE:4303183), partial cds.
AF113019 - Homo sapiens PRO2451 mRNA, complete cds.
BC142963 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2, mRNA (cDNA clone MGC:167047 IMAGE:8860380), complete cds.
JD180975 - Sequence 161999 from Patent EP1572962.
LF328296 - JP 2014500723-A/135799: Polycomb-Associated Non-Coding RNAs.
JD213908 - Sequence 194932 from Patent EP1572962.
JD471097 - Sequence 452121 from Patent EP1572962.
JD550404 - Sequence 531428 from Patent EP1572962.
JD149782 - Sequence 130806 from Patent EP1572962.
JD324855 - Sequence 305879 from Patent EP1572962.
JD207158 - Sequence 188182 from Patent EP1572962.
JD565784 - Sequence 546808 from Patent EP1572962.
LF328297 - JP 2014500723-A/135800: Polycomb-Associated Non-Coding RNAs.
BC136322 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2, mRNA (cDNA clone MGC:167932 IMAGE:9020309), complete cds.
AK303951 - Homo sapiens cDNA FLJ53269 complete cds, highly similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2.
JD103452 - Sequence 84476 from Patent EP1572962.
JD382357 - Sequence 363381 from Patent EP1572962.
JD425843 - Sequence 406867 from Patent EP1572962.
JD446088 - Sequence 427112 from Patent EP1572962.
LF328298 - JP 2014500723-A/135801: Polycomb-Associated Non-Coding RNAs.
AK307944 - Homo sapiens cDNA, FLJ97892.
JD465597 - Sequence 446621 from Patent EP1572962.
AK300939 - Homo sapiens cDNA FLJ59246 complete cds, highly similar to Rattus norvegicus SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 (Smarcd2), mRNA.
JD225501 - Sequence 206525 from Patent EP1572962.
JD294936 - Sequence 275960 from Patent EP1572962.
U66618 - Human SWI/SNF complex 60 KDa subunit (BAF60b) mRNA, complete cds.
JD181234 - Sequence 162258 from Patent EP1572962.
JD252378 - Sequence 233402 from Patent EP1572962.
JD163528 - Sequence 144552 from Patent EP1572962.
JD515337 - Sequence 496361 from Patent EP1572962.
KJ905317 - Synthetic construct Homo sapiens clone ccsbBroadEn_14842 SMARCD2-like gene, encodes complete protein.
LF328299 - JP 2014500723-A/135802: Polycomb-Associated Non-Coding RNAs.
LF328300 - JP 2014500723-A/135803: Polycomb-Associated Non-Coding RNAs.
LF328301 - JP 2014500723-A/135804: Polycomb-Associated Non-Coding RNAs.
LF328302 - JP 2014500723-A/135805: Polycomb-Associated Non-Coding RNAs.
MA563873 - JP 2018138019-A/135799: Polycomb-Associated Non-Coding RNAs.
MA563874 - JP 2018138019-A/135800: Polycomb-Associated Non-Coding RNAs.
MA563875 - JP 2018138019-A/135801: Polycomb-Associated Non-Coding RNAs.
MA563876 - JP 2018138019-A/135802: Polycomb-Associated Non-Coding RNAs.
MA563877 - JP 2018138019-A/135803: Polycomb-Associated Non-Coding RNAs.
MA563878 - JP 2018138019-A/135804: Polycomb-Associated Non-Coding RNAs.
MA563879 - JP 2018138019-A/135805: Polycomb-Associated Non-Coding RNAs.
MA444975 - JP 2018138019-A/16901: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92925 (Reactome details) participates in the following event(s):

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

-  Other Names for This Gene
  Alternate Gene Symbols: A5PLL5, A6NNQ7, B4DV56, B4E1R6, BAF60B, NM_001098426, NP_001091896, PRO2451, Q7L2I6, Q92925, Q9UHZ1, SMRD2_HUMAN
UCSC ID: uc010deb.1
RefSeq Accession: NM_001098426
Protein: Q92925 (aka SMRD2_HUMAN)
CCDS: CCDS45756.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001098426.1
exon count: 13CDS single in 3' UTR: no RNA size: 2770
ORF size: 1596CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3176.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.