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Aliases for HIRA Gene

Aliases for HIRA Gene

  • Histone Cell Cycle Regulator 2 3 5
  • TUP1-Like Enhancer Of Split Protein 1 3 4
  • DiGeorge Critical Region Gene 1 2 3
  • TUPLE1 3 4
  • DGCR1 3 4
  • HIR (Histone Cell Cycle Regulation Defective) Homolog A (S. Cerevisiae) 2
  • HIR Histone Cell Cycle Regulation Defective Homolog A (S. Cerevisiae) 2
  • HIR Histone Cell Cycle Regulation Defective Homolog A 3
  • Protein HIRA 3
  • TUP1 3
  • HIR 4

External Ids for HIRA Gene

Previous HGNC Symbols for HIRA Gene

  • TUPLE1

Previous GeneCards Identifiers for HIRA Gene

  • GC22M016258
  • GC22M017692
  • GC22M002938

Summaries for HIRA Gene

Entrez Gene Summary for HIRA Gene

  • This gene encodes a histone chaperone that preferentially places the variant histone H3.3 in nucleosomes. Orthologs of this gene in yeast, flies, and plants are necessary for the formation of transcriptionally silent heterochomatin. This gene plays an important role in the formation of the senescence-associated heterochromatin foci. These foci likely mediate the irreversible cell cycle changes that occur in senescent cells. It is considered the primary candidate gene in some haploinsufficiency syndromes such as DiGeorge syndrome, and insufficient production of the gene may disrupt normal embryonic development. [provided by RefSeq, Jul 2008]

GeneCards Summary for HIRA Gene

HIRA (Histone Cell Cycle Regulator) is a Protein Coding gene. Diseases associated with HIRA include Digeorge Syndrome and Velocardiofacial Syndrome. Among its related pathways are DNA Damage/Telomere Stress Induced Senescence and Cellular Senescence (REACTOME). Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription corepressor activity.

UniProtKB/Swiss-Prot for HIRA Gene

  • Cooperates with ASF1A to promote replication-independent chromatin assembly. Required for the periodic repression of histone gene transcription during the cell cycle. Required for the formation of senescence-associated heterochromatin foci (SAHF) and efficient senescence-associated cell cycle exit.

Gene Wiki entry for HIRA Gene

Additional gene information for HIRA Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIRA Gene

Genomics for HIRA Gene

GeneHancer (GH) Regulatory Elements for HIRA Gene

Promoters and enhancers for HIRA Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J019429 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.4 +15.7 15676 4.7 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 ZNF263 MRPL40 HIRA TRMT2A DGCR8 UFD1 LINC01311 RPL7AP70 ENSG00000273300 RPL8P5 ESS2
GH22J019446 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 -0.3 -262 2.6 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B C22orf39 HIRA LOC105372860 DGCR8 UFD1 TRMT2A LINC01311 RPL8P5 RPL7AP70 E2F6P1
GH22J019360 Promoter/Enhancer 1.4 EPDnew ENCODE dbSUPER 650.2 +85.8 85799 2.9 HDGF CTCF PKNOX1 EBF1 RELA NFATC1 EED ZNF143 RBM22 ATF7 HIRA UFD1 CLTCL1 DGCR8 LOC105372860 CDC45 TRMT2A LINC01311 E2F6P1 ZDHHC8
GH22J019405 Promoter 0.6 EPDnew 662.6 +41.6 41613 0.1 HNRNPUL1 HIRA UFD1 RPL7AP70 LOC105372860 C22orf39 DGCR11 CDC45 MRPL40 RN7SL168P
GH22J019396 Enhancer 1.2 ENCODE dbSUPER 12.2 +49.8 49765 2.1 HDGF PKNOX1 SMAD1 ATF1 ARNT YY1 TCF12 ZNF766 CBX5 GATA2 DGCR8 TRMT2A UFD1 RPL8P5 ENSG00000273300 E2F6P1 HIRA C22orf39 LOC105372860 LINC01311
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HIRA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIRA gene promoter:
  • TBP
  • AP-1
  • c-Jun
  • ATF-2
  • PPAR-gamma1
  • PPAR-gamma2
  • AML1a
  • USF-1:USF-2
  • Ik-2
  • USF-1

Genomic Locations for HIRA Gene

Genomic Locations for HIRA Gene
116,753 bases
Minus strand
117,004 bases
Minus strand

Genomic View for HIRA Gene

Genes around HIRA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIRA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIRA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIRA Gene

Proteins for HIRA Gene

  • Protein details for HIRA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein HIRA
    Protein Accession:
    Secondary Accessions:
    • Q05BU9
    • Q8IXN2

    Protein attributes for HIRA Gene

    1017 amino acids
    Molecular mass:
    111835 Da
    Quaternary structure:
    • Interacts with histone H3F3B, PAX3 and PAX7 (By similarity). Interacts with CCNA1, HIRIP3, NFU1/HIRIP5 and histone H2B. Part of a complex which includes ASF1A, CABIN1, histone H3.3, histone H4 and UBN1.
    • Sequence=CAA53044.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA54721.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA57436.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HIRA Gene

    Alternative splice isoforms for HIRA Gene


neXtProt entry for HIRA Gene

Post-translational modifications for HIRA Gene

  • Sumoylated.
  • Phosphorylated by CDK2/CCNA1 and CDK2/CCNE1 on Thr-555 in vitro. Also phosphorylated on Thr-555 and Ser-687 in vivo.
  • Ubiquitination at isoforms=2416, isoforms=2381, isoforms=2187, Lys178, and isoforms=227
  • Modification sites at PhosphoSitePlus

Other Protein References for HIRA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIRA Gene

Domains & Families for HIRA Gene

Gene Families for HIRA Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for HIRA Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the WD repeat HIR1 family.
  • Belongs to the WD repeat HIR1 family.
genes like me logo Genes that share domains with HIRA: view

Function for HIRA Gene

Molecular function for HIRA Gene

UniProtKB/Swiss-Prot Function:
Cooperates with ASF1A to promote replication-independent chromatin assembly. Required for the periodic repression of histone gene transcription during the cell cycle. Required for the formation of senescence-associated heterochromatin foci (SAHF) and efficient senescence-associated cell cycle exit.
GENATLAS Biochemistry:
histone cell cycle regulation defective,nuclear localization,S cerevisiae,homolog A,expressed in the neural crest,transcriptional repressors HIR1,HIR2,interacting with core histones H2B and H4,histone binding proteins and PAX1,required for cardiac outflow tract septation,commonly deleted in DiGeorge syndrome (see DGCR,TUPLE1)

Phenotypes From GWAS Catalog for HIRA Gene

Gene Ontology (GO) - Molecular Function for HIRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 CONTRIBUTES_TO DNA binding IBA --
GO:0003700 DNA binding transcription factor activity TAS 9731536
GO:0003714 transcription corepressor activity TAS 9731536
GO:0005515 protein binding IPI 9710638
GO:0031491 CONTRIBUTES_TO nucleosome binding IBA --
genes like me logo Genes that share ontologies with HIRA: view
genes like me logo Genes that share phenotypes with HIRA: view

Human Phenotype Ontology for HIRA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HIRA Gene

MGI Knock Outs for HIRA:
  • Hira Hira<tm1Pjs>
  • Hira Hira<tm1d(EUCOMM)Wtsi>
  • Hira Hira<tm1Aam>
  • Hira Hira<tm2Pjs>
  • Hira Hira<tm1a(EUCOMM)Wtsi>

Animal Model Products

miRNA for HIRA Gene

miRTarBase miRNAs that target HIRA

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for HIRA Gene

Localization for HIRA Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIRA Gene

Nucleus. Nucleus, PML body. Note=Primarily, though not exclusively, localized to the nucleus. Localizes to PML bodies immediately prior to onset of senescence.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HIRA gene
Compartment Confidence
extracellular 5
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HIRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000417 HIR complex IBA --
GO:0000790 nuclear chromatin IDA 14718166
GO:0005634 nucleus IDA,TAS --
GO:0005654 nucleoplasm TAS --
GO:0016605 PML body IEA --
genes like me logo Genes that share ontologies with HIRA: view

Pathways & Interactions for HIRA Gene

genes like me logo Genes that share pathways with HIRA: view

SIGNOR curated interactions for HIRA Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HIRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000070 mitotic sister chromatid segregation IBA --
GO:0001649 osteoblast differentiation IEA --
GO:0006325 chromatin organization IEA --
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with HIRA: view

Drugs & Compounds for HIRA Gene

No Compound Related Data Available

Transcripts for HIRA Gene

mRNA/cDNA for HIRA Gene

(1) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(158) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HIRA Gene

HIR histone cell cycle regulation defective homolog A (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIRA Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b · 16c ^ 17a ·
SP3: - -
SP5: - -
SP6: -
SP7: -
SP10: -

ExUns: 17b ^ 18a · 18b ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b · 22c ^ 23 ^ 24 ^ 25 ^ 26a · 26b
SP6: - - - - - - - - - -

Relevant External Links for HIRA Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HIRA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIRA Gene

Protein differential expression in normal tissues from HIPED for HIRA Gene

This gene is overexpressed in Breast (51.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HIRA Gene

Protein tissue co-expression partners for HIRA Gene

NURSA nuclear receptor signaling pathways regulating expression of HIRA Gene:


SOURCE GeneReport for Unigene cluster for HIRA Gene:


mRNA Expression by UniProt/SwissProt for HIRA Gene:

Tissue specificity: Expressed at high levels in kidney, pancreas and skeletal muscle and at lower levels in brain, heart, liver, lung, and placenta.

Evidence on tissue expression from TISSUES for HIRA Gene

  • Eye(4)
  • Nervous system(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HIRA Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • hypothalamus
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • parathyroid
  • pharynx
  • pituitary gland
  • skull
  • thyroid
  • tongue
  • tooth
  • vocal cord
  • aorta
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • thymus
  • abdominal wall
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • pelvis
  • rectum
  • ureter
  • uterus
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with HIRA: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for HIRA Gene

Orthologs for HIRA Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIRA Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HIRA 34 33
  • 99.77 (n)
(Canis familiaris)
Mammalia HIRA 34 33
  • 91.77 (n)
(Mus musculus)
Mammalia Hira 16 34 33
  • 90.02 (n)
(Bos Taurus)
Mammalia HIRA 34
  • 90 (a)
LOC101906870 33
  • 85.5 (n)
(Rattus norvegicus)
Mammalia Hira 33
  • 89.75 (n)
(Monodelphis domestica)
Mammalia HIRA 34
  • 87 (a)
(Gallus gallus)
Aves HIRA 34 33
  • 77.42 (n)
(Anolis carolinensis)
Reptilia HIRA 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495450 33
  • 73.16 (n)
African clawed frog
(Xenopus laevis)
Amphibia hira 33
(Danio rerio)
Actinopterygii hira 34 33
  • 68.39 (n)
wufb97b07 33
fruit fly
(Drosophila melanogaster)
Insecta Hira 34 35 33
  • 52.59 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009488 33
  • 50.43 (n)
(Caenorhabditis elegans)
Secernentea K10D2.1 34 33
  • 43.02 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HIR1 36 34
  • 26 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons HIRA 33
  • 45.97 (n)
(Oryza sativa)
Liliopsida Os09g0567700 33
  • 46.85 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 41 (a)
Species where no ortholog for HIRA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HIRA Gene

Gene Tree for HIRA (if available)
Gene Tree for HIRA (if available)
Evolutionary constrained regions (ECRs) for HIRA: view image

Paralogs for HIRA Gene

(2) SIMAP similar genes for HIRA Gene using alignment to 4 proteins:

  • F5H4M2_HUMAN
  • H7C2A7_HUMAN
  • L7N2F8_HUMAN Pseudogenes for HIRA Gene

genes like me logo Genes that share paralogs with HIRA: view

No data available for Paralogs for HIRA Gene

Variants for HIRA Gene

Sequence variations from dbSNP and Humsavar for HIRA Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs193920856 uncertain-significance, Malignant tumor of prostate 19,394,344(-) C/T coding_sequence_variant, missense_variant
rs1000008427 -- 19,384,281(-) G/A intron_variant
rs1000109352 -- 19,331,118(-) T/A/C 3_prime_UTR_variant
rs1000115528 -- 19,334,225(-) T/C intron_variant
rs1000124048 -- 19,373,468(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HIRA Gene

Variant ID Type Subtype PubMed ID
esv1126765 CNV insertion 17803354
esv28972 CNV gain 19812545
esv3303776 CNV mobile element insertion 20981092
esv3382059 CNV insertion 20981092
esv3410502 CNV duplication 20981092
esv3575418 CNV gain 25503493
esv3647270 CNV gain 21293372
nsv1160727 CNV duplication 26073780
nsv3557 CNV insertion 18451855
nsv476314 CNV novel sequence insertion 20440878
nsv479571 CNV novel sequence insertion 20440878
nsv588216 CNV gain 21841781
nsv588218 CNV loss 21841781
nsv834123 CNV loss 17160897
nsv834124 CNV loss 17160897
nsv834125 CNV loss 17160897
nsv834127 CNV loss 17160897

Variation tolerance for HIRA Gene

Residual Variation Intolerance Score: 2.64% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIRA Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIRA Gene

Disorders for HIRA Gene

MalaCards: The human disease database

(6) MalaCards diseases for HIRA Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
digeorge syndrome
  • dgs
velocardiofacial syndrome
  • cayler cardiofacial syndrome
chromosomal deletion syndrome
tetralogy of fallot
  • tof
cystic lymphangioma
  • cystic hygroma
- elite association - COSMIC cancer census association via MalaCards
Search HIRA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HIRA

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HIRA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HIRA Gene

Publications for HIRA Gene

  1. A human homolog of the S. cerevisiae HIR1 and HIR2 transcriptional repressors cloned from the DiGeorge syndrome critical region. (PMID: 7633437) Lamour V … Lipinski M (Human molecular genetics 1995) 2 3 4 22 58
  2. Human UBN1 is an ortholog of yeast Hpc2p and has an essential role in the HIRA/ASF1a chromatin-remodeling pathway in senescent cells. (PMID: 19029251) Banumathy G … Adams PD (Molecular and cellular biology 2009) 3 4 22 58
  3. Structure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly. (PMID: 16980972) Tang Y … Marmorstein R (Nature structural & molecular biology 2006) 3 4 22 58
  4. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. (PMID: 15621527) Zhang R … Adams PD (Developmental cell 2005) 3 4 22 58
  5. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. (PMID: 14718166) Tagami H … Nakatani Y (Cell 2004) 3 4 22 58

Products for HIRA Gene

Sources for HIRA Gene

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