U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Pbrm1 polybromo 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306254, updated on 13-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Pbrm1provided by RGD
    Official Full Name
    polybromo 1provided by RGD
    Primary source
    RGD:1565549
    See related
    Ensembl:ENSRNOG00000028227 AllianceGenome:RGD:1565549
    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
    RGD1565549
    Summary
    Predicted to enable chromatin binding activity. Involved in positive regulation of dendritic spine development. Predicted to be located in kinetochore and nucleoplasm. Predicted to be part of RSC-type complex. Human ortholog(s) of this gene implicated in extrahepatic bile duct adenocarcinoma; lung non-small cell carcinoma; lung small cell carcinoma; and renal cell carcinoma. Orthologous to human PBRM1 (polybromo 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 264.5), Spleen (RPKM 189.9) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    16p16
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 16 NC_086034.1 (6219933..6319336)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (6213507..6312895)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (7103714..7202899)

    Chromosome 16 - NC_086034.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD19B Neighboring gene small nucleolar RNA, C/D box 19 Neighboring gene G protein nucleolar 3 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 5 Neighboring gene 5'-nucleotidase domain containing 2 Neighboring gene stabilin 1

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PBRM1 mutation and preliminary response to immune checkpoint blockade treatment in non-small cell lung cancer. Zhou H, et al. NPJ Precis Oncol, 2020. PMID 32195359, Free PMC Article
    2. The genome-wide risk alleles for psychiatric disorders at 3p21.1 show convergent effects on mRNA expression, cognitive function, and mushroom dendritic spine. Yang Z, et al. Mol Psychiatry, 2020 Jan. PMID 31723243
    3. Mutation profiling in cholangiocarcinoma: prognostic and therapeutic implications. Churi CR, et al. PLoS One, 2014. PMID 25536104, Free PMC Article
    4. Genomic alterations of plasma cell-free DNAs in small cell lung cancer and their clinical relevance. Du M, et al. Lung Cancer, 2018 Jun. PMID 29748005
    5. SWI/SNF chromatin remodeling enzymes are associated with cardiac hypertrophy in a genetic rat model of hypertension. Mehrotra A, et al. J Cell Physiol, 2013 Dec. PMID 23702776, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within blastocyst formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within heart development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within placenta development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of dendritic spine development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription elongation by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of RSC-type complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in kinetochore ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    protein polybromo-1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001427685.1 → NP_001414614.1  protein polybromo-1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000016

    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_086034.1 Reference GRCr8

      Range
      6219933..6319336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063275299.1 → XP_063131369.1  protein polybromo-1 isoform X1

    2. XM_063275315.1 → XP_063131385.1  protein polybromo-1 isoform X13

    3. XM_063275317.1 → XP_063131387.1  protein polybromo-1 isoform X14

    4. XM_063275302.1 → XP_063131372.1  protein polybromo-1 isoform X1

    5. XM_063275305.1 → XP_063131375.1  protein polybromo-1 isoform X3

    6. XM_063275308.1 → XP_063131378.1  protein polybromo-1 isoform X5

    7. XM_063275301.1 → XP_063131371.1  protein polybromo-1 isoform X1

    8. XM_063275338.1 → XP_063131408.1  protein polybromo-1 isoform X35

    9. XM_063275298.1 → XP_063131368.1  protein polybromo-1 isoform X1

    10. XM_039095102.2 → XP_038951030.1  protein polybromo-1 isoform X7

      UniProtKB/TrEMBL
      A0A8I5ZMW9
      Conserved Domains (8) summary
      cd05515
      Location:695 → 799
      Bromo_polybromo_V; Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. ...
      cd05517
      Location:203 → 305
      Bromo_polybromo_II; Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. ...
      cd05518
      Location:556 → 659
      Bromo_polybromo_IV; Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. ...
      cd05520
      Location:404 → 505
      Bromo_polybromo_III; Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. ...
      cd05524
      Location:65 → 177
      Bromo_polybromo_I; Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. ...
      cd05526
      Location:812 → 919
      Bromo_polybromo_VI; Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. ...
      cd00084
      Location:1417 → 1481
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
      cd04717
      Location:994 → 1111
      BAH_polybromo; BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional ...

    11. XM_063275320.1 → XP_063131390.1  protein polybromo-1 isoform X17

    12. XM_063275334.1 → XP_063131404.1  protein polybromo-1 isoform X31

    13. XM_063275306.1 → XP_063131376.1  protein polybromo-1 isoform X4

    14. XM_063275311.1 → XP_063131381.1  protein polybromo-1 isoform X9

    15. XM_063275323.1 → XP_063131393.1  protein polybromo-1 isoform X20

    16. XM_063275303.1 → XP_063131373.1  protein polybromo-1 isoform X2

    17. XM_063275310.1 → XP_063131380.1  protein polybromo-1 isoform X8

    18. XM_063275319.1 → XP_063131389.1  protein polybromo-1 isoform X16

    19. XM_063275321.1 → XP_063131391.1  protein polybromo-1 isoform X18

    20. XM_063275335.1 → XP_063131405.1  protein polybromo-1 isoform X32

    21. XM_063275336.1 → XP_063131406.1  protein polybromo-1 isoform X33

    22. XM_063275327.1 → XP_063131397.1  protein polybromo-1 isoform X24

    23. XM_063275312.1 → XP_063131382.1  protein polybromo-1 isoform X10

    24. XM_063275325.1 → XP_063131395.1  protein polybromo-1 isoform X22

    25. XM_063275328.1 → XP_063131398.1  protein polybromo-1 isoform X25

    26. XM_063275339.1 → XP_063131409.1  protein polybromo-1 isoform X36

    27. XM_063275313.1 → XP_063131383.1  protein polybromo-1 isoform X11

    28. XM_063275326.1 → XP_063131396.1  protein polybromo-1 isoform X23

    29. XM_063275329.1 → XP_063131399.1  protein polybromo-1 isoform X26

    30. XM_063275340.1 → XP_063131410.1  protein polybromo-1 isoform X37

    31. XM_063275314.1 → XP_063131384.1  protein polybromo-1 isoform X12

    32. XM_063275316.1 → XP_063131386.1  protein polybromo-1 isoform X13

    33. XM_063275343.1 → XP_063131413.1  protein polybromo-1 isoform X40

    34. XM_063275332.1 → XP_063131402.1  protein polybromo-1 isoform X29

      UniProtKB/TrEMBL
      A0A8I6AV81

    35. XM_063275318.1 → XP_063131388.1  protein polybromo-1 isoform X15

    36. XM_063275333.1 → XP_063131403.1  protein polybromo-1 isoform X30

    37. XM_063275346.1 → XP_063131416.1  protein polybromo-1 isoform X43

    38. XM_063275345.1 → XP_063131415.1  protein polybromo-1 isoform X42

    39. XM_063275304.1 → XP_063131374.1  protein polybromo-1 isoform X3

    40. XM_063275307.1 → XP_063131377.1  protein polybromo-1 isoform X5

    41. XM_063275322.1 → XP_063131392.1  protein polybromo-1 isoform X19

    42. XM_063275324.1 → XP_063131394.1  protein polybromo-1 isoform X21

    43. XM_063275337.1 → XP_063131407.1  protein polybromo-1 isoform X34

    44. XM_063275330.1 → XP_063131400.1  protein polybromo-1 isoform X27

    45. XM_063275341.1 → XP_063131411.1  protein polybromo-1 isoform X38

    46. XM_063275331.1 → XP_063131401.1  protein polybromo-1 isoform X28

    47. XM_063275344.1 → XP_063131414.1  protein polybromo-1 isoform X41

    48. XM_063275309.1 → XP_063131379.1  protein polybromo-1 isoform X6

    49. XM_063275342.1 → XP_063131412.1  protein polybromo-1 isoform X39

    50. XM_063275300.1 → XP_063131370.1  protein polybromo-1 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous