Human Gene SARS1 (uc001dwu.2)
  Description: Homo sapiens seryl-tRNA synthetase (SARS1), transcript variant 1, mRNA.
RefSeq Summary (NM_006513): This gene belongs to the class II amino-acyl tRNA family. The encoded enzyme catalyzes the transfer of L-serine to tRNA (Ser) and is related to bacterial and yeast counterparts. Multiple alternatively spliced transcript variants have been described but the biological validity of all variants is unknown. [provided by RefSeq, Jul 2010].
Transcript (Including UTRs)
   Position: hg19 chr1:109,756,515-109,780,804 Size: 24,290 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:109,756,615-109,780,510 Size: 23,896 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:109,756,515-109,780,804)mRNA (may differ from genome)Protein (514 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
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PubMedReactomeTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYSC_HUMAN
DESCRIPTION: RecName: Full=Serine--tRNA ligase, cytoplasmic; EC=6.1.1.11; AltName: Full=Seryl-tRNA synthetase; Short=SerRS; AltName: Full=Seryl-tRNA(Ser/Sec) synthetase;
FUNCTION: Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).
CATALYTIC ACTIVITY: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
CATALYTIC ACTIVITY: ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec).
PATHWAY: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1.
SUBUNIT: Homodimer. The tRNA molecule binds across the dimer (By similarity).
INTERACTION: Q8IXJ6:SIRT2; NbExp=1; IntAct=EBI-1053431, EBI-477232;
SUBCELLULAR LOCATION: Cytoplasm.
DOMAIN: Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily.

-  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
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.44 RPKM in Cells - Cultured fibroblasts
Total median expression: 1901.43 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 -44.50100-0.445 Picture PostScript Text
3' UTR -97.00294-0.330 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
IPR002314 - aa-tRNA-synt_IIb_cons-dom
IPR006195 - aa-tRNA-synth_II
IPR002317 - Ser-tRNA-ligase_type_1
IPR015866 - Ser-tRNA-synth_1_N
IPR010978 - tRNA-bd_arm

Pfam Domains:
PF00587 - tRNA synthetase class II core domain (G, H, P, S and T)
PF02403 - Seryl-tRNA synthetase N-terminal domain

SCOP Domains:
46589 - tRNA-binding arm
55681 - Class II aaRS and biotin synthetases

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


ModBase Predicted Comparative 3D Structure on P49591
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 DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042803 protein homodimerization activity
GO:0098619 selenocysteine-tRNA ligase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006434 seryl-tRNA aminoacylation
GO:0008033 tRNA processing
GO:0016259 selenocysteine metabolic process
GO:0016525 negative regulation of angiogenesis
GO:0097056 selenocysteinyl-tRNA(Sec) biosynthetic process
GO:1904046 negative regulation of vascular endothelial growth factor production

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  X91257 - H.sapiens mRNA for seryl-tRNA synthetase.
BC111398 - Homo sapiens seryl-tRNA synthetase, mRNA (cDNA clone MGC:104285 IMAGE:4133889), complete cds.
AK312771 - Homo sapiens cDNA, FLJ93186, Homo sapiens seryl-tRNA synthetase (SARS), mRNA.
AK222677 - Homo sapiens mRNA for seryl-tRNA synthetase variant, clone: CBR02289.
BC009390 - Homo sapiens seryl-tRNA synthetase, mRNA (cDNA clone MGC:16732 IMAGE:4129592), complete cds.
BC000716 - Homo sapiens seryl-tRNA synthetase, mRNA (cDNA clone MGC:1285 IMAGE:3505218), complete cds.
D49914 - Homo sapiens mRNA for Seryl tRNA Synthetase, complete cds.
CU679341 - Synthetic construct Homo sapiens gateway clone IMAGE:100019747 5' read SARS mRNA.
AB528307 - Synthetic construct DNA, clone: pF1KB5454, Homo sapiens SARS gene for seryl-tRNA synthetase, without stop codon, in Flexi system.
DQ892144 - Synthetic construct clone IMAGE:100004774; FLH183409.01X; RZPDo839C01142D seryl-tRNA synthetase (SARS) gene, encodes complete protein.
DQ895339 - Synthetic construct Homo sapiens clone IMAGE:100009799; FLH183405.01L; RZPDo839C01141D seryl-tRNA synthetase (SARS) gene, encodes complete protein.
KJ892087 - Synthetic construct Homo sapiens clone ccsbBroadEn_01481 SARS gene, encodes complete protein.
KJ897518 - Synthetic construct Homo sapiens clone ccsbBroadEn_06912 SARS gene, encodes complete protein.
DQ594976 - Homo sapiens piRNA piR-61088, complete sequence.
AK093718 - Homo sapiens cDNA FLJ36399 fis, clone THYMU2009658.
AX748275 - Sequence 1800 from Patent EP1308459.
JD473165 - Sequence 454189 from Patent EP1572962.
JD264089 - Sequence 245113 from Patent EP1572962.
JD255196 - Sequence 236220 from Patent EP1572962.
JD081281 - Sequence 62305 from Patent EP1572962.
JD053796 - Sequence 34820 from Patent EP1572962.
JD082350 - Sequence 63374 from Patent EP1572962.

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

BioCyc Knowledge Library
PWY-6281 - selenocysteine biosynthesis II (archaea and eukaryotes)
TRNA-CHARGING-PWY - tRNA charging pathway

Reactome (by CSHL, EBI, and GO)

Protein P49591 (Reactome details) participates in the following event(s):

R-HSA-379992 serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
R-HSA-2408526 tRNA(Sec) is serylated to Ser-tRNA(Sec) by SARS dimer
R-HSA-379716 Cytosolic tRNA aminoacylation
R-HSA-2408557 Selenocysteine synthesis
R-HSA-379724 tRNA Aminoacylation
R-HSA-2408522 Selenoamino acid metabolism
R-HSA-72766 Translation
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-392499 Metabolism of proteins
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6Y9, NM_006513, NP_006504, P49591, Q5T5C8, Q9NSE3, SARS, SERS, SYSC_HUMAN
UCSC ID: uc001dwu.2
RefSeq Accession: NM_006513
Protein: P49591 (aka SYSC_HUMAN)
CCDS: CCDS795.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006513.3
exon count: 11CDS single in 3' UTR: no RNA size: 1956
ORF size: 1545CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3002.00frame shift in genome: no % Coverage: 99.13
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.