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

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

Summary

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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
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Genomic context

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See Hdac9 in Genome Data Viewer
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

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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. 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

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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

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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)

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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_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

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