Human Gene FARSA (ENST00000314606.9) from GENCODE V44
  Description: Homo sapiens phenylalanyl-tRNA synthetase subunit alpha (FARSA), mRNA. (from RefSeq NM_004461)
RefSeq Summary (NM_004461): Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. This gene encodes a product which is similar to the catalytic subunit of prokaryotic and Saccharomyces cerevisiae phenylalanyl-tRNA synthetases (PheRS). This gene product has been shown to be expressed in a tumor-selective and cell cycle stage- and differentiation-dependent manner, the first member of the tRNA synthetase gene family shown to exhibit this type of regulated expression [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000314606.9
Gencode Gene: ENSG00000179115.11
Transcript (Including UTRs)
   Position: hg38 chr19:12,922,479-12,933,711 Size: 11,233 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg38 chr19:12,922,748-12,933,696 Size: 10,949 Coding Exon Count: 13 

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RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:12,922,479-12,933,711)mRNA (may differ from genome)Protein (508 aa)
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-  Comments and Description Text from UniProtKB
  ID: SYFA_HUMAN
DESCRIPTION: RecName: Full=Phenylalanine--tRNA ligase alpha subunit; EC=6.1.1.20; AltName: Full=CML33; AltName: Full=Phenylalanyl-tRNA synthetase alpha subunit; Short=PheRS;
CATALYTIC ACTIVITY: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
SUBUNIT: Tetramer of two alpha and two beta subunits (By similarity).
INTERACTION: Q9BQ95:ECSIT; NbExp=2; IntAct=EBI-725361, EBI-712452;
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 2 subfamily.
SEQUENCE CAUTION: Sequence=AAB51175.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

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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


-  MalaCards Disease Associations
  MalaCards Gene Search: FARSA
Diseases sorted by gene-association score: sarcocystosis (15), myiasis (12), parasitic ectoparasitic infectious disease (11), theileriasis (6), deafness, autosomal recessive 4, with enlarged vestibular aqueduct (5), spinocerebellar ataxia, autosomal recessive 1 (5), parasitic protozoa infectious disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 45.42 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1027.44 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -96.90269-0.360 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
IPR006195 - aa-tRNA-synth_II
IPR004529 - Phe-tRNA-synth_IIc_asu
IPR002319 - Phenylalanyl-tRNA_Synthase
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF01409 - tRNA synthetases class II core domain (F)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3L4G - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y285
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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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
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MGIRGDEnsemblEnsembl SGD
Protein SequenceProtein SequenceProtein SequenceProtein Sequence Protein Sequence
AlignmentAlignmentAlignmentAlignment Alignment

-  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:0004826 phenylalanine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity

Biological Process:
GO:0006412 translation
GO:0006432 phenylalanyl-tRNA aminoacylation
GO:0043039 tRNA aminoacylation
GO:0051290 protein heterotetramerization

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009328 phenylalanine-tRNA ligase complex
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BC035438 - Homo sapiens phenylalanyl-tRNA synthetase, alpha subunit, mRNA (cDNA clone IMAGE:4747714).
AF042347 - Homo sapiens putative phenylalanyl-tRNA synthetase alpha-subunit mRNA, complete cds.
BC006495 - Homo sapiens phenylalanyl-tRNA synthetase, alpha subunit, mRNA (cDNA clone MGC:1507 IMAGE:2823551), complete cds.
D84471 - Homo sapiens mRNA for phenylalanyl tRNA synthetase beta subunit, complete cds.
U07424 - Human putative tRNA synthetase-like protein mRNA, complete cds.
BC043565 - Homo sapiens phenylalanyl-tRNA synthetase, alpha subunit, mRNA (cDNA clone IMAGE:5214476), partial cds.
AK092093 - Homo sapiens cDNA FLJ34774 fis, clone NT2NE2003309, highly similar to Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20).
AK304587 - Homo sapiens cDNA FLJ50378 complete cds, highly similar to Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20).
AK130195 - Homo sapiens cDNA FLJ26685 fis, clone MPG06479, highly similar to Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20).
JD426476 - Sequence 407500 from Patent EP1572962.
JD439092 - Sequence 420116 from Patent EP1572962.
KJ891146 - Synthetic construct Homo sapiens clone ccsbBroadEn_00540 FARSA gene, encodes complete protein.
BT007198 - Homo sapiens phenylalanine-tRNA synthetase-like mRNA, complete cds.
DQ890745 - Synthetic construct clone IMAGE:100003375; FLH165630.01X; RZPDo839E09160D phenylalanine-tRNA synthetase-like, alpha subunit (FARSLA) gene, encodes complete protein.
DQ893915 - Synthetic construct Homo sapiens clone IMAGE:100008375; FLH165628.01L; RZPDo839E09159D phenylalanine-tRNA synthetase-like, alpha subunit (FARSLA) gene, encodes complete protein.
AB528515 - Synthetic construct DNA, clone: pF1KB5937, Homo sapiens FARSA gene for phenylalanyl-tRNA synthetase, alpha subunit, without stop codon, in Flexi system.
CR456740 - Homo sapiens full open reading frame cDNA clone RZPDo834D0511D for gene FARSLA, phenylalanine-tRNA synthetase-like, alpha subunit; complete cds, incl. stopcodon.
CU675431 - Synthetic construct Homo sapiens gateway clone IMAGE:100020329 5' read FARSA mRNA.
JD025812 - Sequence 6836 from Patent EP1572962.
JD027649 - Sequence 8673 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00970 - Aminoacyl-tRNA biosynthesis

BioCyc Knowledge Library
TRNA-CHARGING-PWY - tRNA charging

Reactome (by CSHL, EBI, and GO)

Protein Q9Y285 (Reactome details) participates in the following event(s):

R-HSA-379848 phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + 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: ENST00000314606.1, ENST00000314606.2, ENST00000314606.3, ENST00000314606.4, ENST00000314606.5, ENST00000314606.6, ENST00000314606.7, ENST00000314606.8, FARS, FARSL, FARSLA, NM_004461, Q9NSD8, Q9Y285, Q9Y4W8, SYFA_HUMAN, uc002mvs.1, uc002mvs.2, uc002mvs.3, uc002mvs.4
UCSC ID: ENST00000314606.9
RefSeq Accession: NM_004461
Protein: Q9Y285 (aka SYFA_HUMAN)
CCDS: CCDS12287.1

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