Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HINT3 Gene

Aliases for HINT3 Gene

  • Histidine Triad Nucleotide Binding Protein 3 2 3 5
  • HINT-3 3 4
  • Histidine Triad Nucleotide-Binding Protein 3 3
  • HIT-Like Protein 3
  • EC 3.-.-.- 4
  • HINT4 3

External Ids for HINT3 Gene

Previous GeneCards Identifiers for HINT3 Gene

  • GC06P125937
  • GC06P126125
  • GC06P126258
  • GC06P126319
  • GC06P126277
  • GC06P123854

Summaries for HINT3 Gene

Entrez Gene Summary for HINT3 Gene

  • Histidine triad proteins, such as HINT3, are nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides (Brenner, 2002 [PubMed 12119013]).[supplied by OMIM, Mar 2008]

GeneCards Summary for HINT3 Gene

HINT3 (Histidine Triad Nucleotide Binding Protein 3) is a Protein Coding gene. GO annotations related to this gene include nucleotide binding and hydrolase activity.

UniProtKB/Swiss-Prot for HINT3 Gene

  • Hydrolyzes phosphoramidate and acyl-adenylate substrates.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HINT3 Gene

Genomics for HINT3 Gene

Regulatory Elements for HINT3 Gene

Enhancers for HINT3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F125788 1.4 FANTOM5 ENCODE 13.8 -164.8 -164818 6.3 HDGF PKNOX1 ARNT CREB3L1 ARID4B FEZF1 ZNF2 ZNF766 ZNF143 FOS HEY2 HINT3 NCOA7-AS1 LOC105377986 NCOA7 TRMT11
GH06F125917 1.4 FANTOM5 ENCODE 13.2 -36.8 -36790 4.3 HDGF ATF1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 HINT3 NCOA7-AS1 NCOA7 PIR57980 PIR42096
GH06F125909 1.2 Ensembl ENCODE 12.7 -44.4 -44363 6.4 PKNOX1 FEZF1 BRCA1 ZNF2 FOS SP3 JUNB TSHZ1 TBX21 ZNF518A HINT3 NCOA7-AS1 CENPW NCOA7 PIR57980 PIR42096
GH06F125843 1.3 FANTOM5 Ensembl ENCODE 10.7 -111.5 -111513 4.4 ZFP64 BACH1 ZNF664 ZNF316 PRDM10 ZNF600 NFE2 MAFK ZBTB20 NFE2L2 NCOA7-AS1 HINT3 HEY2 ENSG00000226409 NCOA7 RN7SKP56
GH06F125922 1 ENCODE 13.2 -32.8 -32774 2.9 PKNOX1 FEZF1 YY1 FOS NCOA1 REST CREB3 SMARCA4 PBX2 STAT3 HINT3 NCOA7-AS1 HEY2 NCOA7 PIR57980 PIR42096
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HINT3 on UCSC Golden Path with GeneCards custom track

Promoters for HINT3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for HINT3 Gene

125,956,715 bp from pter
125,980,244 bp from pter
23,530 bases
Plus strand

Genomic View for HINT3 Gene

Genes around HINT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HINT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HINT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HINT3 Gene

Proteins for HINT3 Gene

  • Protein details for HINT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histidine triad nucleotide-binding protein 3
    Protein Accession:
    Secondary Accessions:
    • B3KQ91
    • Q8N0Y9

    Protein attributes for HINT3 Gene

    182 amino acids
    Molecular mass:
    20361 Da
    Quaternary structure:
    • Forms dimers to octamers and even larger oligomer.

neXtProt entry for HINT3 Gene

Post-translational modifications for HINT3 Gene

  • Ubiquitination at Lys 78, Lys 115, and Lys 179
  • Modification sites at PhosphoSitePlus

Other Protein References for HINT3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HINT3 Gene

Domains & Families for HINT3 Gene

Protein Domains for HINT3 Gene


Suggested Antigen Peptide Sequences for HINT3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 HIT domain.
  • Belongs to the HINT family.
  • Contains 1 HIT domain.
  • Belongs to the HINT family.
genes like me logo Genes that share domains with HINT3: view

No data available for Gene Families for HINT3 Gene

Function for HINT3 Gene

Molecular function for HINT3 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1.5 uM for indolepropinoic acyl-adenylate {ECO:0000269 PubMed:17870088}; KM=22 uM for adenine {ECO:0000269 PubMed:17870088}; KM=29 uM for guanine {ECO:0000269 PubMed:17870088}; KM=32 uM for hypoxanthine {ECO:0000269 PubMed:17870088}; KM=121 uM for uracil {ECO:0000269 PubMed:17870088}; KM=181 uM for cytosine {ECO:0000269 PubMed:17870088}; Note=HINT3 prefers purine over pyrimidine-based substrates.;
UniProtKB/Swiss-Prot Function:
Hydrolyzes phosphoramidate and acyl-adenylate substrates.

Enzyme Numbers (IUBMB) for HINT3 Gene

Gene Ontology (GO) - Molecular Function for HINT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003824 catalytic activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HINT3: view

Phenotypes for HINT3 Gene

genes like me logo Genes that share phenotypes with HINT3: view

Animal Model Products

miRNA for HINT3 Gene

miRTarBase miRNAs that target HINT3

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HINT3 Gene

Localization for HINT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HINT3 Gene

Cytoplasm. Nucleus. Note=Localized as aggregates in the cytoplasm and the nucleus.

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 HINT3 gene
Compartment Confidence
extracellular 5
nucleus 4
cytosol 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for HINT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with HINT3: view

Pathways & Interactions for HINT3 Gene

SuperPathways for HINT3 Gene

No Data Available

Interacting Proteins for HINT3 Gene

STRING Interaction Network Preview (showing 3 interactants - click image to see details)
Selected Interacting proteins: ENSP00000229633 Q9NQE9-HINT3_HUMAN for HINT3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for HINT3 Gene


No data available for Pathways by source and SIGNOR curated interactions for HINT3 Gene

Transcripts for HINT3 Gene

mRNA/cDNA for HINT3 Gene

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

Unigene Clusters for HINT3 Gene

Histidine triad nucleotide binding protein 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HINT3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b
SP1: -
SP2: - -
SP3: -

Relevant External Links for HINT3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HINT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HINT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HINT3 Gene

This gene is overexpressed in Brain (10.5) and Frontal cortex (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HINT3 Gene

Protein tissue co-expression partners for HINT3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HINT3 Gene:


SOURCE GeneReport for Unigene cluster for HINT3 Gene:

genes like me logo Genes that share expression patterns with HINT3: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HINT3 Gene

Orthologs for HINT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for HINT3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HINT3 34 35
  • 99.63 (n)
(Canis familiaris)
Mammalia HINT3 34 35
  • 89.86 (n)
(Bos Taurus)
Mammalia HINT3 34 35
  • 80.26 (n)
(Mus musculus)
Mammalia Hint3 34 16 35
  • 76.04 (n)
(Rattus norvegicus)
Mammalia Hint3 34
  • 74.71 (n)
(Ornithorhynchus anatinus)
Mammalia HINT3 35
  • 74 (a)
(Monodelphis domestica)
Mammalia -- 35
  • 57 (a)
-- 35
  • 54 (a)
(Gallus gallus)
Aves HINT3 34 35
  • 71.7 (n)
(Anolis carolinensis)
Reptilia HINT3 35
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hint3 34
  • 65.78 (n)
(Danio rerio)
Actinopterygii hint3 34 35
  • 60.44 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34015 34 35
  • 52.49 (n)
CG15362 35
  • 29 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007577 34
  • 49.75 (n)
(Caenorhabditis elegans)
Secernentea hint-3 35
  • 26 (a)
Species where no ortholog for HINT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HINT3 Gene

Gene Tree for HINT3 (if available)
Gene Tree for HINT3 (if available)

Paralogs for HINT3 Gene

No data available for Paralogs for HINT3 Gene

Variants for HINT3 Gene

Sequence variations from dbSNP and Humsavar for HINT3 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs10659948 -- 125,978,838(+) CAATA(-/CT)GTTTT utr-variant-3-prime
rs10872305 -- 125,977,223(+) CCCTC(C/T)TTCCC intron-variant
rs111297084 -- 125,969,263(+) ATGGC(A/G)TATTT intron-variant
rs111419715 -- 125,956,539(+) TTTTG(-/T)TTTTT upstream-variant-2KB
rs111803775 -- 125,967,394(+) TGGTG(C/T)AATCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HINT3 Gene

Variant ID Type Subtype PubMed ID
nsv830796 CNV loss 17160897
nsv1025069 CNV loss 25217958
nsv1022677 CNV gain 25217958
nsv1019490 CNV loss 25217958
esv2732681 CNV deletion 23290073

Variation tolerance for HINT3 Gene

Residual Variation Intolerance Score: 59.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.75; 15.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HINT3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HINT3 Gene

Disorders for HINT3 Gene

Relevant External Links for HINT3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HINT3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HINT3 Gene

Publications for HINT3 Gene

  1. Evidence that human histidine triad nucleotide binding protein 3 (Hint3) is a distinct branch of the histidine triad (HIT) superfamily. (PMID: 17870088) Chou T.-F. … Wagner C.R. (J. Mol. Biol. 2007) 3 4 22 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1, and Tfb3. (PMID: 11805111) Bieganowski P. … Brenner C. (J. Biol. Chem. 2002) 2 3 64
  4. Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. (PMID: 12119013) Brenner C. (Biochemistry 2002) 3 4 64
  5. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. (PMID: 27499296) Floyd B.J. … Pagliarini D.J. (Mol. Cell 2016) 3 64

Products for HINT3 Gene

Sources for HINT3 Gene

Loading form....