Human Gene YARS1 (ENST00000373477.9_7) from GENCODE V47lift37
  Description: tyrosyl-tRNA synthetase 1 (from RefSeq NM_003680.4)
Gencode Transcript: ENST00000373477.9_7
Gencode Gene: ENSG00000134684.13_10
Transcript (Including UTRs)
   Position: hg19 chr1:33,240,840-33,282,959 Size: 42,120 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr1:33,241,582-33,282,845 Size: 41,264 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:33,240,840-33,282,959)mRNA (may differ from genome)Protein (528 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYYC_HUMAN
DESCRIPTION: RecName: Full=Tyrosine--tRNA ligase, cytoplasmic; EC=6.1.1.1; AltName: Full=Tyrosyl-tRNA synthetase; Short=TyrRS;
FUNCTION: Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).
CATALYTIC ACTIVITY: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr).
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Cytoplasm.
DISEASE: Defects in YARS are the cause of Charcot-Marie-Tooth disease dominant intermediate type C (CMTDIC) [MIM:608323]. CMTDIC is a form of Charcot-Marie-Tooth disease characterized by clinical and pathologic features intermediate between demyelinating and axonal peripheral neuropathies, and motor median nerve conduction velocities ranging from 25 to 45 m/sec.
SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
SIMILARITY: Contains 1 tRNA-binding domain.
SEQUENCE CAUTION: Sequence=AAB39406.1; Type=Frameshift; Positions=354;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.43 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 544.71 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -50.70114-0.445 Picture PostScript Text
3' UTR -244.84742-0.330 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002305 - aa-tRNA-synth_Ic
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR014729 - Rossmann-like_a/b/a_fold
IPR002547 - tRNA-bd_dom
IPR002307 - Tyr-tRNA-ligase
IPR023617 - Tyr-tRNA-ligase_arc/euk-type

Pfam Domains:
PF00579 - tRNA synthetases class I (W and Y)
PF01588 - Putative tRNA binding domain

SCOP Domains:
50249 - Nucleic acid-binding proteins
52374 - Nucleotidylyl transferase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1N3L - X-ray MuPIT 1NTG - X-ray MuPIT 1Q11 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P54577
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004831 tyrosine-tRNA ligase activity
GO:0004871 signal transducer activity
GO:0005153 interleukin-8 receptor binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity

Biological Process:
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006437 tyrosyl-tRNA aminoacylation
GO:0006915 apoptotic process
GO:0007165 signal transduction

Cellular Component:
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016604 nuclear body
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex
GO:0017102 methionyl glutamyl tRNA synthetase complex


-  Descriptions from all associated GenBank mRNAs
  BC035242 - Homo sapiens tyrosyl-tRNA synthetase, mRNA (cDNA clone IMAGE:4837840).
BC001933 - Homo sapiens tyrosyl-tRNA synthetase, mRNA (cDNA clone MGC:4000 IMAGE:2821104), complete cds.
BC004151 - Homo sapiens tyrosyl-tRNA synthetase, mRNA (cDNA clone MGC:2382 IMAGE:2821104), complete cds.
AK125213 - Homo sapiens cDNA FLJ43223 fis, clone FEBRA2026984, highly similar to Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1).
AK026535 - Homo sapiens cDNA: FLJ22882 fis, clone KAT03587, highly similar to HSU89436 Human tyrosyl-tRNA synthetase mRNA.
BC016689 - Homo sapiens tyrosyl-tRNA synthetase, mRNA (cDNA clone MGC:21917 IMAGE:4386850), complete cds.
AK126444 - Homo sapiens cDNA FLJ44480 fis, clone UTERU2032075, moderately similar to TYROSYL-TRNA SYNTHETASE (EC 6.1.1.1).
AK127182 - Homo sapiens cDNA FLJ45247 fis, clone BRCOC2016661, highly similar to Tyrosyl-tRNA synthetase (EC 6.1.1.1).
AK223608 - Homo sapiens mRNA for tyrosyl-tRNA synthetase variant, clone: FCC132F02.
U89436 - Human tyrosyl-tRNA synthetase mRNA, complete cds.
JD079271 - Sequence 60295 from Patent EP1572962.
KJ892564 - Synthetic construct Homo sapiens clone ccsbBroadEn_01958 YARS gene, encodes complete protein.
KR709439 - Synthetic construct Homo sapiens clone CCSBHm_00002211 YARS (YARS) mRNA, encodes complete protein.
KR709440 - Synthetic construct Homo sapiens clone CCSBHm_00002212 YARS (YARS) mRNA, encodes complete protein.
DQ891666 - Synthetic construct clone IMAGE:100004296; FLH179111.01X; RZPDo839C11130D tyrosyl-tRNA synthetase (YARS) gene, encodes complete protein.
DQ894853 - Synthetic construct Homo sapiens clone IMAGE:100009313; FLH179107.01L; RZPDo839C11129D tyrosyl-tRNA synthetase (YARS) gene, encodes complete protein.
KU178431 - Homo sapiens tyrosyl-tRNA synthetase isoform 1 (YARS) mRNA, partial cds.
KU178432 - Homo sapiens tyrosyl-tRNA synthetase isoform 2 (YARS) mRNA, complete cds, alternatively spliced.
U40714 - Human tyrosyl-tRNA synthetase mRNA, complete cds.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
TRNA-CHARGING-PWY - tRNA charging

Reactome (by CSHL, EBI, and GO)

Protein P54577 (Reactome details) participates in the following event(s):

R-HSA-379980 tyrosine + tRNA(Tyr) + ATP =>Tyr-tRNA(Tyr) + AMP + pyrophosphate
R-HSA-379716 Cytosolic tRNA aminoacylation
R-HSA-379724 tRNA Aminoacylation
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B3KWK4, D3DPQ4, ENST00000373477.1, ENST00000373477.2, ENST00000373477.3, ENST00000373477.4, ENST00000373477.5, ENST00000373477.6, ENST00000373477.7, ENST00000373477.8, NM_003680, O43276, P54577, Q53EN1, SYYC_HUMAN, uc318kuk.1, uc318kuk.2, YARS , YARS1
UCSC ID: ENST00000373477.9_7
RefSeq Accession: NM_003680.4
Protein: P54577 (aka SYYC_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene YARS1:
cmt (Charcot-Marie-Tooth Hereditary Neuropathy Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.