Human Gene CARS1 (ENST00000278224.13_4) from GENCODE V47lift37
  Description: cysteinyl-tRNA synthetase 1, transcript variant 13 (from RefSeq NR_165430.1)
Gencode Transcript: ENST00000278224.13_4
Gencode Gene: ENSG00000110619.18_13
Transcript (Including UTRs)
   Position: hg19 chr11:3,022,159-3,078,648 Size: 56,490 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg19 chr11:3,022,418-3,078,597 Size: 56,180 Coding Exon Count: 22 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:3,022,159-3,078,648)mRNA (may differ from genome)Protein (726 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYCC_HUMAN
DESCRIPTION: RecName: Full=Cysteine--tRNA ligase, cytoplasmic; EC=6.1.1.16; AltName: Full=Cysteinyl-tRNA synthetase; Short=CysRS;
CATALYTIC ACTIVITY: ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys).
COFACTOR: Binds 1 zinc ion per subunit (By similarity).
SUBUNIT: Monomer (By similarity).
SUBCELLULAR LOCATION: Cytoplasm.
DISEASE: Note=A chromosomal aberration involving CARS is associated with inflammatory myofibroblastic tumors (IMTs). Translocation t(2;11)(p23;p15) with ALK.
SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
SEQUENCE CAUTION: Sequence=AAA73901.1; Type=Frameshift; Positions=619;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CARSID484.html";

-  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: 17.92 RPKM in Cells - Cultured fibroblasts
Total median expression: 418.98 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
5' UTR -16.0051-0.314 Picture PostScript Text
3' UTR -69.10259-0.267 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
IPR015803 - Cys-tRNA-ligase
IPR024909 - Cys-tRNA/MSH_ligase
IPR014729 - Rossmann-like_a/b/a_fold
IPR009080 - tRNAsynth_1a_anticodon-bd

Pfam Domains:
PF01406 - tRNA synthetases class I (C) catalytic domain

SCOP Domains:
47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
52374 - Nucleotidylyl transferase
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on P49589
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004817 cysteine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006423 cysteinyl-tRNA aminoacylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK222614 - Homo sapiens mRNA for cysteine-tRNA ligase isoform a variant, clone: CAS12492.
BX647906 - Homo sapiens mRNA; cDNA DKFZp686F1612 (from clone DKFZp686F1612).
BC002880 - Homo sapiens cysteinyl-tRNA synthetase, mRNA (cDNA clone MGC:11246 IMAGE:3940167), complete cds.
AK125503 - Homo sapiens cDNA FLJ43514 fis, clone PERIC2005347.
AK126135 - Homo sapiens cDNA FLJ44147 fis, clone THYMU2028041, highly similar to Homo sapiens cysteinyl-tRNA synthetase (CARS).
AB208814 - Homo sapiens mRNA for cysteine-tRNA ligase isoform b variant protein.
AK296763 - Homo sapiens cDNA FLJ59563 complete cds, highly similar to Cysteinyl-tRNA synthetase (EC 6.1.1.16).
AK096313 - Homo sapiens cDNA FLJ38994 fis, clone NT2RI2009259, highly similar to Cysteinyl-tRNA synthetase (EC 6.1.1.16).
AK295371 - Homo sapiens cDNA FLJ59524 complete cds, highly similar to Cysteinyl-tRNA synthetase (EC 6.1.1.16).
AK298514 - Homo sapiens cDNA FLJ54534 complete cds, highly similar to Homo sapiens cysteinyl-tRNA synthetase (CARS), transcript variant 3, mRNA.
AK302644 - Homo sapiens cDNA FLJ54741 complete cds, highly similar to Homo sapiens cysteinyl-tRNA synthetase (CARS), transcript variant 3, mRNA.
L06845 - Human cysteinyl-tRNA synthetase mRNA, partial cds.
JD257539 - Sequence 238563 from Patent EP1572962.
JD550784 - Sequence 531808 from Patent EP1572962.
AF288206 - Homo sapiens cytoplasmic cysteinyl-tRNA synthetase mRNA, complete cds.
AF288207 - Homo sapiens cysteinyl-tRNA synthetase mRNA, complete cds, alternatively spliced.
KJ890825 - Synthetic construct Homo sapiens clone ccsbBroadEn_00219 CARS gene, encodes complete protein.
BT009913 - Homo sapiens cysteinyl-tRNA synthetase mRNA, complete cds.
DQ890773 - Synthetic construct clone IMAGE:100003403; FLH165837.01X; RZPDo839H05160D cysteinyl-tRNA synthetase (CARS) gene, encodes complete protein.
JD171370 - Sequence 152394 from Patent EP1572962.
JD049682 - Sequence 30706 from Patent EP1572962.
AK308005 - Homo sapiens cDNA, FLJ97953.
AK289432 - Homo sapiens cDNA FLJ75536 partial cds, highly similar to Homo sapiens cysteinyl-tRNA synthetase (CARS), transcript variant1, mRNA.
CU678270 - Synthetic construct Homo sapiens gateway clone IMAGE:100017796 5' read CARS mRNA.
AK131221 - Homo sapiens cDNA FLJ16116 fis, clone ADRGL2000056.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P49589 (Reactome details) participates in the following event(s):

R-HSA-379887 cysteine + tRNA(Cys) + ATP => Cys-tRNA(Cys) + 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: CARS, CARS1 , ENST00000278224.1, ENST00000278224.10, ENST00000278224.11, ENST00000278224.12, ENST00000278224.2, ENST00000278224.3, ENST00000278224.4, ENST00000278224.5, ENST00000278224.6, ENST00000278224.7, ENST00000278224.8, ENST00000278224.9, NR_165430, P49589, Q53XI8, Q5HYE4, Q9HD24, Q9HD25, SYCC_HUMAN, uc317jod.1
UCSC ID: ENST00000278224.13_4
RefSeq Accession: NM_139273.4
Protein: P49589 (aka SYCC_HUMAN)

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