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Pbrm1 polybromo 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 306254, updated on 4-Jan-2025

Summary

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Official Symbol
Pbrm1provided by RGD
Official Full Name
polybromo 1provided by RGD
Primary source
RGD:1565549
See related
EnsemblRapid: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 and SWI/SNF 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, Jan 2025]
Expression
Biased expression in Thymus (RPKM 264.5), Spleen (RPKM 189.9) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Pbrm1 in Genome Data Viewer
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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. 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
  2. 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
  3. Mutation profiling in cholangiocarcinoma: prognostic and therapeutic implications. Churi CR, et al. PLoS One, 2014. PMID 25536104, Free PMC Article
  4. 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
  5. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Varela I, et al. Nature, 2011 Jan 27. PMID 21248752, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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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

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Preferred Names
protein polybromo-1

NCBI Reference Sequences (RefSeq)

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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
    UniProtKB/TrEMBL
    A0A8I5ZMW9
    Related
    ENSRNOP00000079535.2, ENSRNOT00000094186.2

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9
    Related
    ENSRNOP00000104472.1, ENSRNOT00000136414.1

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

  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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    D3ZT52
    Related
    ENSRNOP00000016581.8, ENSRNOT00000016581.10

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    D3ZT52

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    D3ZT52

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

    UniProtKB/TrEMBL
    A0A8I6AR61
    Related
    ENSRNOP00000096705.2, ENSRNOT00000096494.2

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9
    Related
    ENSRNOP00000106061.1, ENSRNOT00000147340.1

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

    UniProtKB/TrEMBL
    A0A8I6G5U9
    Related
    ENSRNOP00000081368.1, ENSRNOT00000109995.2

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

    UniProtKB/TrEMBL
    A0A8I6AR61, A0A8I6AV81
    Related
    ENSRNOP00000092107.2, ENSRNOT00000104141.2

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9
    Related
    ENSRNOP00000112238.1, ENSRNOT00000137529.1

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    D3ZT52

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I6AR61

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9

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

    UniProtKB/TrEMBL
    A0A8I6G5U9

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

    UniProtKB/TrEMBL
    A0A8I5ZMW9
Nucleotide Protein Strain
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