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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.

Additional gene information for HINT3 Gene

No data available for CIViC summary , 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
GH06H125788 1.7 FANTOM5 ENCODE dbSUPER 13.8 -164.8 -164818 6 HDGF PKNOX1 FOXA2 ARNT ARID4B FEZF1 ZNF2 ZNF766 ZNF143 FOS HEY2 RNF217 HINT3 NCOA7-AS1 LOC105377986 NCOA7 TRMT11
GH06H125917 1.7 FANTOM5 ENCODE dbSUPER 13.2 -36.8 -36790 4 HDGF FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 HINT3 NCOA7-AS1 NCOA7 PIR57980 PIR42096
GH06H125909 1.5 Ensembl ENCODE dbSUPER 12.7 -44.4 -44363 6 PKNOX1 ATF1 FEZF1 BRCA1 ZNF2 TCF12 ATF7 FOS RUNX3 SP3 HINT3 NCOA7-AS1 CENPW NCOA7 PIR57980 PIR42096
GH06H125797 1.4 Ensembl ENCODE dbSUPER 11.1 -158.1 -158062 1 HDGF PKNOX1 TBL1XR1 BMI1 FEZF1 BATF ZNF350 ATF7 RUNX3 IKZF2 NCOA7-AS1 HINT3 NCOA7
GH06H125867 1.3 Ensembl ENCODE dbSUPER 11.9 -88.1 -88063 2 FEZF1 RFX5 ZNF366 SCRT2 ZNF350 RCOR1 ZNF362 CEBPB OVOL3 ZNF843 HINT3 NCOA7-AS1 HEY2 RN7SKP56
- 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
ENSR00000202281 585 1801 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3 NFYC ZC3H11A

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 posLast=7878, isoforms=115, and isoforms=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

Gene Families for HINT3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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



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

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

CRISPR Products

miRNA for HINT3 Gene

miRTarBase miRNAs that target HINT3

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for HINT3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
  • Mitochondria (2)
See all subcellular structures

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

Gene Ontology (GO) - Biological Process for HINT3 Gene


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

Drugs & Compounds for HINT3 Gene

No Compound Related Data Available

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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for HINT3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 CGAP 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:


Evidence on tissue expression from TISSUES for HINT3 Gene

  • Eye(4.1)
  • Nervous system(2.7)
genes like me logo Genes that share expression patterns with HINT3: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.63 (n)
(Canis familiaris)
Mammalia HINT3 33 34
  • 89.86 (n)
(Bos Taurus)
Mammalia HINT3 33 34
  • 80.26 (n)
(Mus musculus)
Mammalia Hint3 33 16 34
  • 76.04 (n)
(Rattus norvegicus)
Mammalia Hint3 33
  • 74.71 (n)
(Ornithorhynchus anatinus)
Mammalia HINT3 34
  • 74 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 57 (a)
-- 34
  • 54 (a)
(Gallus gallus)
Aves HINT3 33 34
  • 71.7 (n)
(Anolis carolinensis)
Reptilia HINT3 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hint3 33
  • 65.78 (n)
(Danio rerio)
Actinopterygii hint3 33 34
  • 60.44 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34015 34 33
  • 52.49 (n)
CG15362 34
  • 29 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007577 33
  • 49.75 (n)
(Caenorhabditis elegans)
Secernentea hint-3 34
  • 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
rs1000001503 -- 125,955,576(+) TGGCA(A/T)AACTC upstream-variant-2KB
rs1000058867 -- 125,976,534(+) TTTTT(G/T)CAAAG intron-variant
rs1000080182 -- 125,957,704(+) TCAAA(C/T)TATTA intron-variant
rs1000094350 -- 125,978,367(+) CTAAT(A/G)ACATA utr-variant-3-prime
rs1000305483 -- 125,964,759(+) ACACA(C/G)ACACA intron-variant

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

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

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 TF … Wagner CR (Journal of molecular biology 2007) 3 4 22 60
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  3. 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 60
  4. Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1, and Tfb3. (PMID: 11805111) Bieganowski P … Brenner C (The Journal of biological chemistry 2002) 2 3 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for HINT3 Gene

Sources for HINT3 Gene

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