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VARS2 Gene

protein-coding   GIFtS: 49

GC06P030992
valyl-tRNA synthetase 2, mitochondrial (putative)
(Previous names: valyl-tRNA synthetase 2-like, valyl-tRNA synthetase like )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: VARS2L, VARSL)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
DKFZP434L1435 1
EC 6.1.1.9 3
Em:AB023048.4 1
G7A 5
KIAA1885 1, 3
MGC138259 2
MGC142165 2
OTTHUMP00000062434 2
VARS 5
VARS1 5
VARS2L 2, 3
VARSL 2, 3
ValRS 3
Descriptions
Valine--tRNA ligase 3
Valyl-tRNA synthetase-like 3
valine tRNA ligase 2, mitochondrial (putative) 2
valyl-tRNA synthetase 2, mitochondrial 2
valyl-tRNA synthetase 2, mitochondrial (putative) 2
valyl-tRNA synthetase 2-like 1, 2
valyl-tRNA synthetase like 1, 2
External Ids
HGNC: 216421
Entrez Gene: 571762
UniProtKB: Q5ST303
Ensembl: ENSG000001374117
Search outside databases for aliases for VARS2 gene

Previous GC identifers: GC06M031816 GC06M031516 GC06M031851 GC06M031852 GC06M031853 GC06Pc31014

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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  --
(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.33   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.33

VARS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P030992:     (about GC identifiers)

Start:
30,989,961 bp from pter
End:
31,002,212 bp from pter
Size:
12,252 bases
Orientation:
plus strand

2 alternative locations:
Chr6+,c6_COX 31,019,107-31,031,210      Chr6+,c6_QBL 31,014,423-31,026,685     
RefSeq DNA sequence:
NC_000006.10  NT_007592.14  NT_113891.1  NT_113893.1  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: SYVM_HUMAN, Q5ST30 (See protein sequence)
Recommended Name: Valyl-tRNA synthetase, mitochondrial precursor  
Size: 1063 amino acids; 118462 Da
Subcellular location: Mitochondrion (Potential)
Sequence caution: Sequence=BAD92716.1; Type=Miscellaneous discrepancy; Note=The sequence differs
from that shown because it seems to be derived from a pre-mRNA; Sequence=CAM24842.1;
Type=Erroneous gene model prediction; Sequence=CAM25404.1; Type=Erroneous gene model prediction;
Sequence=CAQ06763.1; Type=Erroneous gene model prediction; Sequence=CAQ09774.1; Type=Erroneous
gene model prediction; Sequence=CAQ10925.1; Type=Erroneous gene model prediction;
Secondary accessions: A2ABL7 Q2M2A0 Q59FI1 Q5SQ96 Q5SS98 Q6DKJ5 Q6ZV24 Q96GN2 Q96H77 Q96Q02 Q9H6R2
Q9UFH7
Alternative splicing: 2 isoforms:  Q5ST30-1   Q5ST30-2   

REFSEQ proteins: NP_065175.3  

ENSEMBL proteins: 
ENSP00000316092 ENSP00000365483 


Human Recombinant Proteins 
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Browse Abnova for Human Recombinant Proteins
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005737 cytoplasm IEA--
GO:0005739 mitochondrion IEA--
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Antibodies for VARS2: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Browse Antibodies at Sigma-Aldrich
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Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
Browse Abnova for Monoclonal and Polyclonal Antibodies
Search Novus for antibodies for VARS2

Assays for VARS2: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

5/6 InterPro domains/families (see all 6 ):
 IPR001412 aa-tRNA-synth_I_CS
 IPR002303 Val-tRNA_synth_Ia
 IPR014729 Rossmann-like_a/b/a_fold
 IPR013155 V/L/I-tRNA-synth_anticodon-bd
 IPR002300 aa-tRNA-synth_Ia


   GeneDecks  VARS2 for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q5ST30

ProtoNet protein and cluster: Q5ST30

3 Blocks protein families:
IPB002300 Aminoacyl-tRNA synthetase
IPB002303 Valyl-tRNA synthetase signature
IPB013155 tRNA synthetase


UniProtKB/Swiss-Prot: SYVM_HUMAN, Q5ST30
Similarity: Belongs to the class-I aminoacyl-tRNA synthetase family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (VARS2)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020442

              Applied Biosystems Silencer® siRNAs for VARS2

              Sigma-Aldrich siRNA for VARS2  
                     Sigma-Aldrich shRNA for VARS2  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_020442
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_020442
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_020442 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_020442

UniProtKB/Swiss-Prot: SYVM_HUMAN, Q5ST30
Catalytic activity: ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)
Enzyme Number (IUBMB): EC 6.1.1.9 

Genatlas biochemistry entry for VARS2:
valyl-tRNA synthetase 2,same as G7a,see HTFAG@

4 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0000166 nucleotide binding IEA--
GO:0004832 valine-tRNA ligase activity IEA--
GO:0005524 ATP binding IEA--
GO:0016874 ligase activity IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section


2 Kegg Pathways  (Kegg details for VARS2):
 hsa00290 Valine, leucine and isoleucine biosynthesis
 hsa00970 Aminoacyl-tRNA biosynthesis

   GeneDecks  VARS2 for the pathways selected above  
About GeneDecksing

3 Interacting proteins for VARS2 (ENSP000003160923) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
ENSG00000137343ENSP000003656623STRING (score=.712)
ENSG00000146112ENSP000002748533STRING (score=.706)
MRPS18BENSP000002598733STRING (score=.706)
About this table

1 Gene Ontology (GO) biological process term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006438 valyl-tRNA aminoacylation IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for VARS2

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (VARS2)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020442

              Sigma-Aldrich siRNA for VARS2  
                     Sigma-Aldrich shRNA for VARS2  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_020442  

REFSEQ mRNAs for VARS2 gene: 

NM_020442.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_020442  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_020442
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_020442
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_020442 

Additional cDNA sequence: 

AB067472.1 AK000511.1 AK025618.1 AK026063.1 AK094483.1 AK125069.1 AK293780.1 AK294451.1 
AK303415.1 AK304807.1 AK315733.1 AL122037.1 BC008844.2 BC009355.2 BC063427.1 BC073838.1 
BC112054.1 BC113605.1 BC143534.1 BC143535.1 BC143536.1 

10 DOTS entries:

DT.414330  DT.99956622  DT.97848345  DT.101967025  DT.100783857  DT.100783864  DT.100783861  DT.121348680 
DT.100783856  DT.95370180 

24/149 AceView cDNA sequences (see all 149 ):

BQ065288 BQ642051 BQ065988 BM827439 BQ057625 BQ059035 BQ063810 BQ641944 
BQ065373 BQ063639 Z38986 BQ061568 BQ061525 AA496582 BQ061610 BQ056176 
BQ062109 BQ064294 BQ054908 BG910473 BQ055455 AI708217 BX095238 M78120 

Unigene Cluster for VARS2:

Valyl-tRNA synthetase 2, mitochondrial (putative)
Hs.597526  [show with all ESTs]
Unigene Representative Sequence: AB067472


GeneLoc Exon Structure

5/10 Alternative Splicing Database (ASD) splice patterns (SP) for VARS2 (see all 10 )

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b · 13c ^ 14a ·
SP1:        -     -                 -                 -     -                                   -                                                               
SP2:                                                                                            -                                                               
SP3:                                -                 -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -               
SP4:              -                 -                                                                                                                           
SP5:                                -                 -     -                                                                                                   

ExUns: 14b · 14c
SP1:            
SP2:            
SP3:            
SP4:            
SP5:            

About this scheme

ECgene alternative splicing isoforms for VARS2

2 Ensembl transcripts including schematic representations:
ENST00000321897  ENST00000376306  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

VARS2 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for VARS2

1 / 2

6 probe-sets matching VARS2 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
41371_at2 U95-A 4 0.88 0.22 0.91 0.86 -- -- -- -- --

46573_at2 U95-B 1 0.81 1.00 0.79 1.14 -- -- -- -- --

226200_at2 U133-B 1 1.00 1.00 -- -- -- -- -- -- --

203577_at2 U133-A 4 1.00 0.25 -- -- -- -- -- -- --

226200_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

203577_at2 U133Plus2 4 1.00 0.25 -- -- -- -- -- -- --
GeneDecks  VARS2 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: GAGCTGCAGG

SOURCE GeneReport for Unigene cluster: Hs.597526
(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for VARS2 gene from 5/7 species (see all 7 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
VARS1   -- valyl-tRNA synthetase 86.48(n)
85.54(a)
474833  XM_532063.2  XP_532063.2 
chimpanzee
(Pan troglodytes)
VARS1   -- valyl-tRNA synthetase 97.38(n)
96.68(a)
462550  XM_518340.2  XP_518340.2 
rat
(Rattus norvegicus)
Vars21   -- valyl-tRNA synthetase 2, mitochondrial (putative) 84.28(n)
84.25(a)
309596  NM_213563.1  NP_998728.1 
mouse
(Mus musculus)
Vars21, 5 175
valyl-tRNA synthetase 2, mitochondrial (putative)1, 5 84.38(n)1
84.44(a)1
689151  NM_175137.31  NP_780346.21 
 AI0469555  AI4616095  (see all 26)
zebrafish
(Danio rerio)
LOC5584551   -- similar to valyl-tRNA synthetase 2-like 57.73(n)
54.54(a)
558455  XM_681668.3  XP_686760.3 
About this table        Species with no ortholog for VARS2

ENSEMBL Gene Tree for VARS2
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for VARS2 gene
VARS2  IARS2  IARS22  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/116 NCBI SNPs in VARS2 are shown (see all 116 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 111)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 6 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs12643031,2
A,C,F,H30990492(-) TTTCCT/CGTCTC 1 -- ut51 ese39Minor allele frequency- C:0.21NS EU EA WA 1010
rs93940211,2
A,C,F,H31001106(+) TCTCCG/AAGCCA 1 Q/R mis1 ese313Minor allele frequency- A:0.40NA EA NS EU WA 1366
rs22494641,2
A,C,F,H30996140(-) GCCCCG/ATTCAC 1 R/W mis115Minor allele frequency- A:0.37EA EU WA NS MN 2962
rs20745061,2
A,C,F,H30998462(-) CAGCAC/ACTGGG 1 L/V mis18Minor allele frequency- A:0.21EA EU WA NA 2038
rs46781,2
A,C,F,H31001920(-) GCTGCC/TGGAGG 1 Q/R mis1 ese316Minor allele frequency- T:0.12EU EA WA NS MN NA 1610
rs32188311,2
C,F,H30990410(+) GATACC/TATGCA 1 -- ut519Minor allele frequency- T:0.02NS EU EA WA 1016
rs22528631,2
C,F,H31001407(-) TGCTGC/TGCCTG 1 A/T mis1 ese38Minor allele frequency- T:0.33EA WA EU 2206
rs25329361,2
C,F,H31002387(-) GAAAGT/GAGGTA 1 -- ng318Minor allele frequency- G:0.25EU EA WA MN NA 650
rs69267231,2
C,F,H30990782(+) TAGCAG/AGGGAG 1 R/G mis1 ese38Minor allele frequency- A:0.28EU EA WA 820
rs25329371,2
C,F31002323(-) TCCAGC/TGAGGA 1 -- ng315Minor allele frequency- T:0.22EA MN NA 1126
About this table

HapMap Linkage Disequilibrium images for VARS2 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 192150

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

7 PubMed articles for VARS2 gene:
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 57176 HGNC: 21642 AceView: VARS2L Ensembl:ENSG00000137411 euGenes: HUgn57176
ECgene: VARS2 H-InvDB: VARS2
(According to HUGE)
About This Section

HUGE: KIAA1885
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

  --
(Available from WIS Yeda, Salk, Tufts)
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  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for VARS2:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
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  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for VARS2-related products

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for VARS2 Browse antibodies at Sigma-Aldrich
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for VARS2 Browse small molecules at Sigma-Aldrich
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