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Aliases for HARS Gene

Aliases for HARS Gene

  • Histidyl-TRNA Synthetase 2 3 4 5
  • EC 6.1.1.21 4 61
  • HisRS 3 4
  • HRS 3 4
  • Histidine TRNA Ligase 1, Cytoplasmic 2
  • Histidine--TRNA Ligase, Cytoplasmic 3
  • Histidine Translase 3
  • CMT2W 3
  • USH3B 3

External Ids for HARS Gene

Previous GeneCards Identifiers for HARS Gene

  • GC05M139869
  • GC05M140036
  • GC05M140081
  • GC05M140034
  • GC05M135198

Summaries for HARS Gene

Entrez Gene Summary for HARS Gene

  • Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. The protein encoded by this gene is a cytoplasmic enzyme which belongs to the class II family of aminoacyl-tRNA synthetases. The enzyme is responsible for the synthesis of histidyl-transfer RNA, which is essential for the incorporation of histidine into proteins. The gene is located in a head-to-head orientation with HARSL on chromosome five, where the homologous genes share a bidirectional promoter. The gene product is a frequent target of autoantibodies in the human autoimmune disease polymyositis/dermatomyositis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for HARS Gene

HARS (Histidyl-TRNA Synthetase) is a Protein Coding gene. Diseases associated with HARS include Usher Syndrome Type 3B and Charcot-Marie-Tooth Disease, Axonal, Type 2W. Among its related pathways are Gene Expression and tRNA Aminoacylation. GO annotations related to this gene include nucleotide binding and histidine-tRNA ligase activity. An important paralog of this gene is HARS2.

UniProtKB/Swiss-Prot for HARS Gene

  • Cytoplasmic histidine--tRNA ligase (Probable). Plays a role in axon guidance.

Gene Wiki entry for HARS Gene

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

Genomics for HARS Gene

Regulatory Elements for HARS Gene

Enhancers for HARS 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
GH05G140710 1.2 ENCODE 21.1 -19.0 -18960 1.9 CREB3L1 FEZF1 YY1 ZNF143 ZNF263 SP3 TBX21 SSRP1 ZNF610 GLIS1 PCDHA4 HARS HDAC3 PCDHA5 LOC102723915 PCDHA2 PCDHA1 PCDHA10 PCDHA3 IGIP
GH05G140344 1.6 FANTOM5 ENCODE dbSUPER 11.8 +344.9 344923 5.8 PKNOX1 SIN3A ARID4B ZNF2 FOS ZNF263 SP3 REST ZNF592 SMARCA4 SRA1 HARS PFDN1 HBEGF APBB3 CD14 PCDHA7 ANKHD1 ENSG00000253965
GH05G141039 1.6 FANTOM5 Ensembl ENCODE 10.8 -348.5 -348511 2.6 PKNOX1 ATF1 ARID4B SIN3A ZNF48 YY1 ELK1 CBX5 ZNF143 KLF7 PCDHB16 PCDHA4 PCDHA1 PCDHA2 HARS PCDHA9 PCDHA5 PCDHA8 PCDHA7 PCDHB7
GH05G140594 1.4 FANTOM5 Ensembl ENCODE 10.9 +96.0 96024 4.0 CREB3L1 TAF1 MAX CEBPG ZIC2 RAD21 YY1 ZNF766 CREM MIER1 CD14 APBB3 SRA1 TMCO6 PCDHA1 PCDHA2 HARS SLC35A4 PCDHA5 EIF4EBP3
GH05G140717 1.2 ENCODE 12 -27.1 -27113 2.7 MLX CREB3L1 ZNF416 ZNF263 SP3 PPARGC1A MEF2D GLIS1 RCOR2 NBN HDAC3 TMCO6 PURA LOC102723915 PCDHA3 IGIP PCDHB3 PCDHB9 PCDHB7 PCDHB15
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HARS on UCSC Golden Path with GeneCards custom track

Promoters for HARS Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187817 324 1801 HDGF PKNOX1 CREB3L1 ARNT WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for HARS Gene

Chromosome:
5
Start:
140,673,173 bp from pter
End:
140,692,024 bp from pter
Size:
18,852 bases
Orientation:
Minus strand

Genomic View for HARS Gene

Genes around HARS on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HARS Gene

Proteins for HARS Gene

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

    Protein Symbol:
    P12081-SYHC_HUMAN
    Recommended name:
    Histidine--tRNA ligase, cytoplasmic
    Protein Accession:
    P12081
    Secondary Accessions:
    • B4DHQ1
    • B4DY73
    • D6REN6
    • J3KNE5

    Protein attributes for HARS Gene

    Size:
    509 amino acids
    Molecular mass:
    57411 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAA28956.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HARS Gene

    Alternative splice isoforms for HARS Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HARS Gene

Selected DME Specific Peptides for HARS Gene

P12081:
  • GLGDLKLLFEYL
  • REFYQCD
  • GKYGEDSKLIY
  • LKTPKGT
  • GLDYYTG
  • KLLKLKAQLG
  • ICSSVDKLDK
  • VAAGGRYD
  • LWDAGIKAELLYKKNPKLLNQLQYCEE
  • KGLAPEVADRIGD
  • VPCVGLSIGVERIF
  • RTTETQV
  • DLTVPFAR
  • LRYDLTVPF
  • CFKRHGA
  • GGRYDGL
  • IMCEILS
  • VRGLKQQKASA

Post-translational modifications for HARS Gene

  • Ubiquitination at isoforms=475 and isoforms=2, 3, 4230
  • Modification sites at PhosphoSitePlus

Domains & Families for HARS Gene

Gene Families for HARS Gene

Graphical View of Domain Structure for InterPro Entry

P12081

UniProtKB/Swiss-Prot:

SYHC_HUMAN :
  • Belongs to the class-II aminoacyl-tRNA synthetase family.
Family:
  • Belongs to the class-II aminoacyl-tRNA synthetase family.
genes like me logo Genes that share domains with HARS: view

Function for HARS Gene

Molecular function for HARS Gene

GENATLAS Biochemistry:
histidyl-tRNA synthetase,target autoantibodies in the immune disease polymyositis/dermatomyositis
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
UniProtKB/Swiss-Prot Function:
Cytoplasmic histidine--tRNA ligase (Probable). Plays a role in axon guidance.

Enzyme Numbers (IUBMB) for HARS Gene

Gene Ontology (GO) - Molecular Function for HARS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004812 aminoacyl-tRNA ligase activity IEA --
GO:0004821 histidine-tRNA ligase activity TAS --
GO:0005524 ATP binding IEA --
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with HARS: view
genes like me logo Genes that share phenotypes with HARS: view

Human Phenotype Ontology for HARS Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for HARS Gene

Localization for HARS Gene

Subcellular locations from UniProtKB/Swiss-Prot for HARS Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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 HARS gene
Compartment Confidence
cytosol 5
mitochondrion 3
nucleus 3

Gene Ontology (GO) - Cellular Components for HARS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA,IEA 21464306
GO:0005739 mitochondrion IBA --
GO:0005829 cytosol TAS,IDA --
genes like me logo Genes that share ontologies with HARS: view

Pathways & Interactions for HARS Gene

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

Pathways by source for HARS Gene

1 BioSystems pathway for HARS Gene
1 KEGG pathway for HARS Gene

Gene Ontology (GO) - Biological Process for HARS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation NAS 7755634
GO:0006418 tRNA aminoacylation for protein translation TAS,IEA --
GO:0006427 histidyl-tRNA aminoacylation IEA --
GO:0032543 mitochondrial translation IBA --
genes like me logo Genes that share ontologies with HARS: view

No data available for SIGNOR curated interactions for HARS Gene

Drugs & Compounds for HARS Gene

(5) Drugs for HARS Gene - From: DrugBank, ClinicalTrials, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Histidine Approved Nutra Target 0
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0
Hormones Pharma 14415

(1) Additional Compounds for HARS Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with HARS: view

Transcripts for HARS Gene

Unigene Clusters for HARS Gene

Histidyl-tRNA synthetase:
Representative Sequences:

Inhibitory RNA Products

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

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c · 6d ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a ·
SP1: - - - - -
SP2: - - - - - - -
SP3: - - - - -
SP4: - - - - -
SP5: - - - - - - - - - - -
SP6: - -
SP7: - - -
SP8: -
SP9:
SP10:
SP11:
SP12:

ExUns: 11b · 11c ^ 12 ^ 13a · 13b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for HARS Gene

GeneLoc Exon Structure for
HARS
ECgene alternative splicing isoforms for
HARS

Expression for HARS Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HARS Gene

This gene is overexpressed in Lymph node (11.7) and Peripheral blood mononuclear cells (7.6).

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



Protein tissue co-expression partners for HARS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HARS Gene:

HARS

SOURCE GeneReport for Unigene cluster for HARS Gene:

Hs.528050

mRNA Expression by UniProt/SwissProt for HARS Gene:

P12081-SYHC_HUMAN
Tissue specificity: Brain, heart, liver and kidney.

Evidence on tissue expression from TISSUES for HARS Gene

  • Nervous system(5)
  • Lung(4.6)
  • Liver(4.3)
  • Skin(3.2)
  • Kidney(2.4)
  • Intestine(2.2)
  • Muscle(2.2)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • head
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns with HARS: view

Primer Products

No data available for mRNA differential expression in normal tissues for HARS Gene

Orthologs for HARS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HARS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HARS 34 35
  • 99.74 (n)
cow
(Bos Taurus)
Mammalia HARS 34 35
  • 90.83 (n)
dog
(Canis familiaris)
Mammalia HARS 34 35
  • 90.7 (n)
oppossum
(Monodelphis domestica)
Mammalia HARS 35
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hars 34
  • 88.85 (n)
mouse
(Mus musculus)
Mammalia Hars 34 16 35
  • 88.34 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 74 (a)
OneToMany
-- 35
  • 58 (a)
OneToMany
chicken
(Gallus gallus)
Aves HARS 34 35
  • 77.29 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 73 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489846 34
  • 67.92 (n)
Str.5457 34
zebrafish
(Danio rerio)
Actinopterygii hars 34 35
  • 73.22 (n)
Dr.4161 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10028 34
fruit fly
(Drosophila melanogaster)
Insecta CG6335 36
  • 63 (a)
Aats-his 34 35
  • 62.65 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000735 34
  • 61.18 (n)
worm
(Caenorhabditis elegans)
Secernentea hars-1 34 35
  • 57.59 (n)
hrs-1 36
  • 53 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR187W 34
  • 56.76 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E06381g 34
  • 54.91 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HTS1 34 35 37
  • 54.34 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G02760 34
  • 58.18 (n)
rice
(Oryza sativa)
Liliopsida Os05g0150900 34
  • 58.12 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8844 35
  • 63 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU06914 34
  • 58.47 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes hrs1 34
  • 55.15 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3858 34
Species where no ortholog for HARS was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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 HARS Gene

ENSEMBL:
Gene Tree for HARS (if available)
TreeFam:
Gene Tree for HARS (if available)

Paralogs for HARS Gene

Paralogs for HARS Gene

(2) SIMAP similar genes for HARS Gene using alignment to 7 proteins:

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

Variants for HARS Gene

Sequence variations from dbSNP and Humsavar for HARS Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs143473232 Pathogenic, Charcot-Marie-Tooth disease 2W (CMT2W) [MIM:616625] 140,679,789(+) ATACA(A/C/G)TGAGG intron-variant, reference, missense
rs191391414 Pathogenic, Charcot-Marie-Tooth disease 2W (CMT2W) [MIM:616625] 140,679,114(+) AATAC(C/T)GAGCA intron-variant, reference, missense
rs387906639 Pathogenic, Usher syndrome 3B (USH3B) [MIM:614504] 140,674,776(-) ACAGT(A/C)CTGTG upstream-variant-2KB, reference, missense
rs536175170 Charcot-Marie-Tooth disease 2W (CMT2W) [MIM:616625] 140,677,671(+) TGTCT(A/G)CTGAG reference, missense
rs747156884 Charcot-Marie-Tooth disease 2W (CMT2W) [MIM:616625] 140,674,274(+) GAGGG(A/G)CTGGC downstream-variant-500B, upstream-variant-2KB, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv830508 CNV loss 17160897
nsv964945 CNV duplication 23825009

Variation tolerance for HARS Gene

Residual Variation Intolerance Score: 43.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.77; 47.13% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HARS Gene

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

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

Disorders for HARS Gene

MalaCards: The human disease database

(12) MalaCards diseases for HARS Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome type 3b
  • ush3b
charcot-marie-tooth disease, axonal, type 2w
  • charcot-marie-tooth disease, axonal type 2w
usher syndrome, type 3a
  • usher syndrome type 3
polymyositis
  • pm
myositis
  • inflammatory disorder of muscle
- elite association - COSMIC cancer census association via MalaCards
Search HARS in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SYHC_HUMAN
  • Charcot-Marie-Tooth disease 2W (CMT2W) [MIM:616625]: An autosomal dominant, axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. CMT2W patients manifest a peripheral neuropathy mainly affecting the lower limbs and resulting in gait difficulties and distal sensory impairment. Most patients also have upper limb involvement. {ECO:0000269 PubMed:22930593, ECO:0000269 PubMed:26072516}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Usher syndrome 3B (USH3B) [MIM:614504]: A syndrome characterized by progressive vision and hearing loss during early childhood. Some patients have the so-called Charles Bonnet syndrome, involving decreased visual acuity and vivid visual hallucinations. USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH3 is characterized by postlingual, progressive hearing loss, variable vestibular dysfunction, and onset of retinitis pigmentosa symptoms, including nyctalopia, constriction of the visual fields, and loss of central visual acuity, usually by the second decade of life. {ECO:0000269 PubMed:22279524}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HARS

Human Genome Epidemiology (HuGE) Navigator
HARS
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HARS
genes like me logo Genes that share disorders with HARS: view

No data available for Genatlas for HARS Gene

Publications for HARS Gene

  1. A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS. (PMID: 7755634) O'Hanlon T.P. … Miller F.W. (Biochem. Biophys. Res. Commun. 1995) 3 4 22 64
  2. Transcriptional analyses of the gene region that encodes human histidyl-tRNA synthetase: identification of a novel bidirectional regulatory element. (PMID: 8406012) Tsui H.W. … Tsui F.W.L. (Gene 1993) 3 4 22 64
  3. Human histidyl-tRNA synthetase: recognition of amino acid signature regions in class 2a aminoacyl-tRNA synthetases. (PMID: 1549469) Raben N. … Plotz P. (Nucleic Acids Res. 1992) 3 4 22 64
  4. Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies. (PMID: 26072516) Safka Brozkova D. … Baets J. (Brain 2015) 3 4 64
  5. A loss-of-function variant in the human histidyl-tRNA synthetase (HARS) gene is neurotoxic in vivo. (PMID: 22930593) Vester A. … Antonellis A. (Hum. Mutat. 2013) 3 4 64

Products for HARS Gene

Sources for HARS Gene

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