Human Gene FARS2 (uc003mwr.2) Description and Page Index
  Description: Homo sapiens phenylalanyl-tRNA synthetase 2, mitochondrial (FARS2), nuclear gene encoding mitochondrial protein, mRNA.
RefSeq Summary (NM_006567): This gene encodes a protein that transfers phenylalanine to its cognate tRNA. This protein localizes to the mitochondrion and plays a role in mitochondrial protein translation. Mutations in this gene can cause combined oxidative phosphorylation deficiency 14 (Alpers encephalopathy). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016].
Transcript (Including UTRs)
   Position: hg19 chr6:5,261,584-5,771,816 Size: 510,233 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr6:5,368,804-5,771,662 Size: 402,859 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:5,261,584-5,771,816)mRNA (may differ from genome)Protein (451 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SYFM_HUMAN
DESCRIPTION: RecName: Full=Phenylalanine--tRNA ligase, mitochondrial; EC=6.1.1.20; AltName: Full=Phenylalanyl-tRNA synthetase; Short=PheRS; Flags: Precursor;
FUNCTION: Catalyzes direct attachment of p-Tyr (Tyr) to tRNAPhe. Permits also, with a lower efficiency, the attachment of m-Tyr to tRNAPhe, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins.
CATALYTIC ACTIVITY: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Mitochondrion matrix (Potential).
SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
SIMILARITY: Contains 1 FDX-ACB domain.
SEQUENCE CAUTION: Sequence=AAF28998.1; Type=Frameshift; Positions=414;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FARS2
CDC HuGE Published Literature: FARS2
Positive Disease Associations: Alcoholism , Body Height , Fibrinogen , Heart Failure
Related Studies:
  1. Alcoholism
    , , . [PubMed 0]
  2. Body Height
    Amidou N'Diaye et al. PLoS genetics 2011, Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry., PLoS genetics. [PubMed 21998595]
  3. Fibrinogen
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: FARS2
Diseases sorted by gene-association score: combined oxidative phosphorylation deficiency 14* (1691), spastic paraplegia 77, autosomal recessive* (1629), combined oxidative phosphorylation deficiency (48), mitochondrial dna depletion syndrome 4a (7)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.86 RPKM in Testis
Total median expression: 199.26 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 -132.90331-0.402 Picture PostScript Text
3' UTR -35.93154-0.233 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
IPR004530 - Phe-tRNA-synth_IIc_mito
IPR002319 - Phenylalanyl-tRNA_Synthase
IPR005121 - PheS_beta_Fdx_antiC-bd

Pfam Domains:
PF01409 - tRNA synthetases class II core domain (F)
PF03147 - Ferredoxin-fold anticodon binding domain

SCOP Domains:
55681 - Class II aaRS and biotin synthetases
54991 - Anticodon-binding domain of PheRS

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

3CMQ
- X-ray MuPIT

3HFV
- X-ray MuPIT

3TEG
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3TUP - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95363
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
 Gene Details Gene DetailsGene DetailsGene Details
 Gene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0000166 nucleotide 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:0006418 tRNA aminoacylation for protein translation
GO:0006432 phenylalanyl-tRNA aminoacylation
GO:0008033 tRNA processing
GO:0043039 tRNA aminoacylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  AK312454 - Homo sapiens cDNA, FLJ92809, highly similar to Homo sapiens phenylalanine-tRNA synthetase 1 (mitochondrial)(FARS1), nuclear gene encoding mitochondrial protein, mRNA.
LF384912 - JP 2014500723-A/192415: Polycomb-Associated Non-Coding RNAs.
AK223423 - Homo sapiens mRNA for phenylalanine-tRNA synthetase 2 variant, clone: FCC110D03.
BC020239 - Homo sapiens phenylalanyl-tRNA synthetase 2, mitochondrial, mRNA (cDNA clone MGC:31969 IMAGE:5258249), complete cds.
BC021112 - Homo sapiens phenylalanyl-tRNA synthetase 2, mitochondrial, mRNA (cDNA clone MGC:31883 IMAGE:5088776), complete cds.
BC014273 - Homo sapiens mRNA similar to phenylalanine-tRNA synthetase (cDNA clone IMAGE:3845369).
AF097441 - Homo sapiens phenylalanine-tRNA synthetase (FARS1) mRNA, nuclear gene encoding mitochondrial protein, complete cds.
CR542279 - Homo sapiens full open reading frame cDNA clone RZPDo834F0926D for gene FARS1, phenylalanine-tRNA synthetase 1 (mitochondrial); complete cds, without stopcodon.
AF161438 - Homo sapiens HSPC320 mRNA, partial cds.
MA620489 - JP 2018138019-A/192415: Polycomb-Associated Non-Coding RNAs.
CU676830 - Synthetic construct Homo sapiens gateway clone IMAGE:100021980 5' read FARS2 mRNA.
AK001146 - Homo sapiens cDNA FLJ10284 fis, clone HEMBB1001346, weakly similar to Homo sapiens phenylalanine-tRNA synthetase mRNA.
JD107888 - Sequence 88912 from Patent EP1572962.
JD535400 - Sequence 516424 from Patent EP1572962.
JD433664 - Sequence 414688 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 pathway

Reactome (by CSHL, EBI, and GO)

Protein O95363 (Reactome details) participates in the following event(s):

R-HSA-380203 phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
R-HSA-379726 Mitochondrial 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: B2R664, FARS1, HSPC320, NM_006567, NP_006558, O95363, Q53F66, Q5TCS3, Q6FG29, Q9NPY7, Q9P062, SYFM_HUMAN
UCSC ID: uc003mwr.2
RefSeq Accession: NM_006567
Protein: O95363 (aka SYFM_HUMAN)
CCDS: CCDS4494.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene FARS2:
fars2-def (FARS2 Deficiency)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006567.3
exon count: 7CDS single in 3' UTR: no RNA size: 1841
ORF size: 1356CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2714.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.