U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Hdac9 histone deacetylase 9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 687001, updated on 3-Apr-2024

    Summary

    Go to the top of the page Help
    Symbol
    Hdac9provided by RGD
    Full Name
    histone deacetylase 9provided by RGD
    Primary source
    RGD:1310748
    See related
    Ensembl:ENSRNOG00000004158 AllianceGenome:RGD:1310748
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    MITR; RGD1310748; RGD1563092
    Summary
    Predicted to enable several functions, including enzyme binding activity; histone deacetylase activity (H4-K16 specific); and transcription corepressor activity. Involved in neuron differentiation and response to amphetamine. Located in nucleus. Biomarker of middle cerebral artery infarction. Orthologous to human HDAC9 (histone deacetylase 9). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 53.7), Heart (RPKM 45.8) 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:
    6q16
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (56489472..57351654, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (50762074..51624311, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (53487367..54358694, complement)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120093244 Neighboring gene twist family bHLH transcription factor 1 Neighboring gene developmental pluripotency-associated 4, pseudogene 4 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene phosphoribosyl pyrophosphate synthetase 1-like 1 Neighboring gene sorting nexin 13

    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. HDAC9 is an epigenetic repressor of kidney angiotensinogen establishing a sex difference. Bourgeois CT, et al. Biol Sex Differ, 2017. PMID 28572913, Free PMC Article
    2. HDAC9 exacerbates endothelial injury in cerebral ischaemia/reperfusion injury. Shi W, et al. J Cell Mol Med, 2016 Jun. PMID 26865248, Free PMC Article
    3. Histone deacetylase 9 inhibition upregulates microRNA-92a to repress the progression of intracranial aneurysm via silencing Bcl-2-like protein 11. Cai Y, et al. J Drug Target, 2021 Aug. PMID 33480300
    4. Nucleocytoplasmic translocation of HDAC9 regulates gene expression and dendritic growth in developing cortical neurons. Sugo N, et al. Eur J Neurosci, 2010 May. PMID 20525066
    5. miR-383-5p Regulated by the Transcription Factor CTCF Affects Neuronal Impairment in Cerebral Ischemia by Mediating Deacetylase HDAC9 Activity. Shen J, et al. Mol Neurobiol, 2022 Oct. PMID 35927544

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Knockdown of histone deacetylase 9 attenuates sepsis-induced myocardial injury and inflammatory response.
      Title: Knockdown of histone deacetylase 9 attenuates sepsis-induced myocardial injury and inflammatory response.
    2. miR-383-5p Regulated by the Transcription Factor CTCF Affects Neuronal Impairment in Cerebral Ischemia by Mediating Deacetylase HDAC9 Activity.
      Title: miR-383-5p Regulated by the Transcription Factor CTCF Affects Neuronal Impairment in Cerebral Ischemia by Mediating Deacetylase HDAC9 Activity.
    3. Histone deacetylase 9 inhibition upregulates microRNA-92a to repress the progression of intracranial aneurysm via silencing Bcl-2-like protein 11.
      Title: Histone deacetylase 9 inhibition upregulates microRNA-92a to repress the progression of intracranial aneurysm via silencing Bcl-2-like protein 11.
    4. Results indicate that histone deacetylase 9 is a novel suppressing factor involved in angiotensinogen (AGT) regulation in renal proximal tubular cells, leading to low levels of intrarenal AGT in females.
      Title: HDAC9 is an epigenetic repressor of kidney angiotensinogen establishing a sex difference.
    5. HDAC9 is one of critical components of a signal transduction pathway that links cerebral injury to epigenetic modification in the brain.
      Title: HDAC9 exacerbates endothelial injury in cerebral ischaemia/reperfusion injury.
    6. findings indicate that chromatin remodeling with nucleocytoplasmic translocation of HDAC9 regulates activity-dependent gene expression and dendritic growth in developing cortical neurons
      Title: Nucleocytoplasmic translocation of HDAC9 regulates gene expression and dendritic growth in developing cortical neurons.
    Submit: New GeneRIF Correction

    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 transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K14 deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K9 deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H4K16 deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT enables histone deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein kinase C binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein lysine deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to insulin stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cholesterol homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within determination of adult lifespan ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within heart development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in positive regulation of cell migration involved in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of skeletal muscle fiber development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of skeletal muscle fiber differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to amphetamine IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of histone deacetylase complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of histone methyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    histone deacetylase 9
    Names
    MEF2-interacting transcriptional repressor
    NP_001186974.1
    XP_008762836.2
    XP_008762837.2
    XP_008762838.2
    XP_017449851.1
    XP_017449852.1
    XP_017449854.1
    XP_017449857.1
    XP_017449860.1
    XP_038968868.1
    XP_038968873.1
    XP_038968874.1
    XP_038968877.1
    XP_038968882.1
    XP_038968883.1
    XP_038968884.1
    XP_038968885.1
    XP_063118552.1
    XP_063118553.1
    XP_063118554.1
    XP_063118555.1
    XP_063118556.1
    XP_063118557.1
    XP_063118558.1
    XP_063118559.1
    XP_063118561.1
    XP_063118562.1
    XP_063118563.1
    XP_063118564.1
    XP_063118565.1
    XP_063118566.1
    XP_063118567.1
    XP_063118569.1
    XP_063118570.1
    XP_063118571.1
    XP_063118572.1
    XP_063118573.1
    XP_063118574.1

    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_001200045.1 → NP_001186974.1  histone deacetylase 9

      See identical proteins and their annotated locations for NP_001186974.1

      Status: PROVISIONAL

      Source sequence(s)
      AB558551
      UniProtKB/TrEMBL
      A0A8I5ZWP6, E5RQ38, F1MA74
      Related
      ENSRNOP00000005521.6, ENSRNOT00000005521.8
      Conserved Domains (2) summary
      cd10163
      Location:38 → 127
      ClassIIa_HDAC9_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase
      cd11681
      Location:633 → 1010
      HDAC_classIIa; Histone deacetylases, class IIa

    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_086024.1 Reference GRCr8

      Range
      56489472..57351654 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063262499.1 → XP_063118569.1  histone deacetylase 9 isoform X15

    2. XM_063262495.1 → XP_063118565.1  histone deacetylase 9 isoform X11

    3. XM_063262482.1 → XP_063118552.1  histone deacetylase 9 isoform X1

    4. XM_063262487.1 → XP_063118557.1  histone deacetylase 9 isoform X6

    5. XM_008764614.4 → XP_008762836.2  histone deacetylase 9 isoform X14

      UniProtKB/TrEMBL
      A0A8I5ZWP6

    6. XM_017594363.3 → XP_017449852.1  histone deacetylase 9 isoform X5

      UniProtKB/TrEMBL
      A0A8I5ZWP6

    7. XM_063262497.1 → XP_063118567.1  histone deacetylase 9 isoform X13

    8. XM_017594362.3 → XP_017449851.1  histone deacetylase 9 isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZWP6

    9. XM_063262496.1 → XP_063118566.1  histone deacetylase 9 isoform X12

    10. XM_017594365.3 → XP_017449854.1  histone deacetylase 9 isoform X11

      UniProtKB/TrEMBL
      A0A8I5ZWP6

    11. XM_063262484.1 → XP_063118554.1  histone deacetylase 9 isoform X2

    12. XM_063262501.1 → XP_063118571.1  histone deacetylase 9 isoform X18

    13. XM_008764616.4 → XP_008762838.2  histone deacetylase 9 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZWP6

    14. XM_063262486.1 → XP_063118556.1  histone deacetylase 9 isoform X5

    15. XM_063262483.1 → XP_063118553.1  histone deacetylase 9 isoform X1

    16. XM_063262488.1 → XP_063118558.1  histone deacetylase 9 isoform X7

      UniProtKB/TrEMBL
      E5RQ38, F1MA74

    17. XM_063262485.1 → XP_063118555.1  histone deacetylase 9 isoform X3

    18. XM_039112956.1 → XP_038968884.1  histone deacetylase 9 isoform X19

      Conserved Domains (1) summary
      cd11681
      Location:315 → 692
      HDAC_classIIa; Histone deacetylases, class IIa

    19. XM_039112940.2 → XP_038968868.1  histone deacetylase 9 isoform X3

      UniProtKB/TrEMBL
      A0A8I5ZWP6
      Conserved Domains (2) summary
      cd10163
      Location:57 → 146
      ClassIIa_HDAC9_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase
      cd11681
      Location:652 → 1029
      HDAC_classIIa; Histone deacetylases, class IIa

    20. XM_039112945.1 → XP_038968873.1  histone deacetylase 9 isoform X7

      UniProtKB/TrEMBL
      A0A8I5ZWP6, E5RQ38, F1MA74
      Conserved Domains (2) summary
      cd10163
      Location:38 → 127
      ClassIIa_HDAC9_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase
      cd11681
      Location:633 → 1010
      HDAC_classIIa; Histone deacetylases, class IIa

    21. XM_039112946.2 → XP_038968874.1  histone deacetylase 9 isoform X8

      UniProtKB/TrEMBL
      A0A0G2K082
      Conserved Domains (1) summary
      cd11681
      Location:631 → 1008
      HDAC_classIIa; Histone deacetylases, class IIa

    22. XM_063262494.1 → XP_063118564.1  histone deacetylase 9 isoform X10

    23. XM_063262489.1 → XP_063118559.1  histone deacetylase 9 isoform X7

      UniProtKB/TrEMBL
      E5RQ38, F1MA74

    24. XM_039112957.1 → XP_038968885.1  histone deacetylase 9 isoform X19

      Conserved Domains (1) summary
      cd11681
      Location:315 → 692
      HDAC_classIIa; Histone deacetylases, class IIa

    25. XM_063262500.1 → XP_063118570.1  histone deacetylase 9 isoform X16

    26. XM_063262492.1 → XP_063118562.1  histone deacetylase 9 isoform X7

      UniProtKB/TrEMBL
      E5RQ38, F1MA74

    27. XM_039112955.1 → XP_038968883.1  histone deacetylase 9 isoform X19

      Conserved Domains (1) summary
      cd11681
      Location:315 → 692
      HDAC_classIIa; Histone deacetylases, class IIa

    28. XM_039112949.2 → XP_038968877.1  histone deacetylase 9 isoform X9

      UniProtKB/TrEMBL
      A0A0G2K082
      Conserved Domains (1) summary
      cd11681
      Location:621 → 998
      HDAC_classIIa; Histone deacetylases, class IIa

    29. XM_063262491.1 → XP_063118561.1  histone deacetylase 9 isoform X7

      UniProtKB/TrEMBL
      E5RQ38, F1MA74

    30. XM_039112954.2 → XP_038968882.1  histone deacetylase 9 isoform X17

      UniProtKB/TrEMBL
      A0A0G2K082
      Conserved Domains (1) summary
      cd11681
      Location:600 → 977
      HDAC_classIIa; Histone deacetylases, class IIa

    31. XM_063262493.1 → XP_063118563.1  histone deacetylase 9 isoform X10

    32. XM_063262503.1 → XP_063118573.1  histone deacetylase 9 isoform X21

    33. XM_008764615.4 → XP_008762837.2  histone deacetylase 9 isoform X25

      UniProtKB/TrEMBL
      A0A8I6AB01

    34. XM_017594368.3 → XP_017449857.1  histone deacetylase 9 isoform X23

      UniProtKB/TrEMBL
      A0A8I6AB01

    35. XM_017594371.3 → XP_017449860.1  histone deacetylase 9 isoform X24

      UniProtKB/TrEMBL
      A0A8I6AB01
      Related
      ENSRNOP00000090853.1

    36. XM_063262504.1 → XP_063118574.1  histone deacetylase 9 isoform X22

    37. XM_063262502.1 → XP_063118572.1  histone deacetylase 9 isoform X20

    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