Human Gene PBRM1 (uc003der.2)
  Description: Homo sapiens polybromo 1 (PBRM1), mRNA.
RefSeq Summary (NM_018313): This locus encodes a subunit of ATP-dependent chromatin-remodeling complexes. The encoded protein has been identified as in integral component of complexes necessary for ligand-dependent transcriptional activation by nuclear hormone receptors. Mutations at this locus have been associated with primary clear cell renal cell carcinoma. [provided by RefSeq, Feb 2012].
Transcript (Including UTRs)
   Position: hg19 chr3:52,579,368-52,713,739 Size: 134,372 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr3:52,582,079-52,713,727 Size: 131,649 Coding Exon Count: 28 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:52,579,368-52,713,739)mRNA (may differ from genome)Protein (1602 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PBRM1
CDC HuGE Published Literature: PBRM1
Positive Disease Associations: Adiponectin , major mood disorders: bipolar, major depression , Mood Disorders , Respiratory Function Tests
Related Studies:
  1. Adiponectin
    Zari Dastani et al. PLoS genetics 2012, Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals., PLoS genetics. [PubMed 22479202]
  2. Adiponectin
    Zari Dastani et al. PLoS genetics 2012, Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals., PLoS genetics. [PubMed 22479202]
  3. major mood disorders: bipolar, major depression
    McMahon ,et al. Nat Genet 2010, Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1 , Nature genetics 2010 42- 2 : 128-31. [PubMed 20081856]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PBRM1
Diseases sorted by gene-association score: renal clear cell carcinoma* (423), renal cell carcinoma* (169), clear cell renal cell carcinoma (29), clear cell papillary renal cell carcinoma* (14), collecting duct carcinoma (13), kidney cancer (5), intrahepatic cholangiocarcinoma (3)
* = 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: 10.41 RPKM in Ovary
Total median expression: 330.95 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
3' UTR -677.962711-0.250 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
  Pfam Domains:
PF00439 - Bromodomain
PF00505 - HMG (high mobility group) box
PF01426 - BAH domain
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box
47370 - Bromodomain

ModBase Predicted Comparative 3D Structure on Q86U86-3
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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 orthologNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
   FlyBaseWormBase 
   Protein SequenceProtein Sequence 
   AlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  LF385534 - JP 2014500723-A/193037: Polycomb-Associated Non-Coding RNAs.
AF197569 - Homo sapiens BAF180 (BAF180) mRNA, complete cds.
LP955726 - Sequence 8 from Patent WO2017214373.
AY281068 - Homo sapiens polybromo-1D (PB1) mRNA, complete cds.
AF177387 - Homo sapiens polybromo-1 (PB1) mRNA, complete cds, alternatively spliced.
AF225870 - Homo sapiens polybromo-1 (PB1) mRNA, complete cds, alternatively spliced.
AF225871 - Homo sapiens polybromo-1 (PB1) mRNA, complete cds, alternatively spliced.
AF225872 - Homo sapiens polybromo-1 (PB1) mRNA, complete cds, alternatively spliced.
BC115009 - Homo sapiens polybromo 1, mRNA (cDNA clone MGC:131576 IMAGE:7962003), complete cds.
BC115010 - Homo sapiens polybromo 1, mRNA (cDNA clone IMAGE:7962007), partial cds.
BC115011 - Homo sapiens polybromo 1, mRNA (cDNA clone MGC:131579 IMAGE:7962010), complete cds.
BC116450 - Homo sapiens cDNA clone IMAGE:7962011, containing frame-shift errors.
BC129934 - Homo sapiens polybromo 1, mRNA (cDNA clone MGC:156155 IMAGE:40082629), complete cds.
BC129935 - Homo sapiens polybromo 1, mRNA (cDNA clone MGC:156156 IMAGE:40082630), complete cds.
AK056541 - Homo sapiens cDNA FLJ31979 fis, clone NT2RP7008441, highly similar to Polybromo 1 protein.
MA621111 - JP 2018138019-A/193037: Polycomb-Associated Non-Coding RNAs.
MB474740 - JP 2019527037-A/8: DIAGNOSTIC AND THERAPEUTIC METHODS FOR CANCER.
LF209991 - JP 2014500723-A/17494: Polycomb-Associated Non-Coding RNAs.
AF130061 - Homo sapiens clone FLB6914 PRO1821 mRNA, complete cds.
LF333725 - JP 2014500723-A/141228: Polycomb-Associated Non-Coding RNAs.
AL050083 - Homo sapiens mRNA; cDNA DKFZp566K1246 (from clone DKFZp566K1246).
BC089409 - Homo sapiens polybromo 1, mRNA (cDNA clone IMAGE:3066268), partial cds.
AK001507 - Homo sapiens cDNA FLJ10645 fis, clone NT2RP2005767, moderately similar to G.gallus PB1 gene.
LF333724 - JP 2014500723-A/141227: Polycomb-Associated Non-Coding RNAs.
JD565854 - Sequence 546878 from Patent EP1572962.
LF333723 - JP 2014500723-A/141226: Polycomb-Associated Non-Coding RNAs.
BC015323 - Homo sapiens polybromo 1, mRNA (cDNA clone IMAGE:4397664), complete cds.
LF333722 - JP 2014500723-A/141225: Polycomb-Associated Non-Coding RNAs.
JD044463 - Sequence 25487 from Patent EP1572962.
KJ906218 - Synthetic construct Homo sapiens clone ccsbBroadEn_15888 PBRM1 gene, encodes complete protein.
CU677259 - Synthetic construct Homo sapiens gateway clone IMAGE:100018805 5' read PB1 mRNA.
LF333721 - JP 2014500723-A/141224: Polycomb-Associated Non-Coding RNAs.
LF333712 - JP 2014500723-A/141215: Polycomb-Associated Non-Coding RNAs.
AK001926 - Homo sapiens cDNA FLJ11064 fis, clone PLACE1004824.
BC070273 - Homo sapiens cDNA clone IMAGE:6714197, partial cds.
MA445568 - JP 2018138019-A/17494: Polycomb-Associated Non-Coding RNAs.
MA569302 - JP 2018138019-A/141228: Polycomb-Associated Non-Coding RNAs.
MA569301 - JP 2018138019-A/141227: Polycomb-Associated Non-Coding RNAs.
MA569300 - JP 2018138019-A/141226: Polycomb-Associated Non-Coding RNAs.
MA569299 - JP 2018138019-A/141225: Polycomb-Associated Non-Coding RNAs.
MA569298 - JP 2018138019-A/141224: Polycomb-Associated Non-Coding RNAs.
MA569289 - JP 2018138019-A/141215: Polycomb-Associated Non-Coding RNAs.

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

Protein Q86U86 (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: AF225870, BAF180, NM_018313, NP_060783, PB1, Q86U86-3
UCSC ID: uc003der.2
RefSeq Accession: NM_018313
Protein: Q86U86-3, splice isoform of Q86U86 CCDS: CCDS43099.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF225870.1
exon count: 28CDS single in 3' UTR: no RNA size: 4885
ORF size: 4809CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9818.00frame 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.