Human Gene LGALS2 (uc003ata.3)
  Description: Homo sapiens lectin, galactoside-binding, soluble, 2 (LGALS2), mRNA.
RefSeq Summary (NM_006498): The protein encoded by this gene is a soluble beta-galactoside binding lectin. The encoded protein is found as a homodimer and can bind to lymphotoxin-alpha. A single nucleotide polymorphism in an intron of this gene can alter the transcriptional level of the protein, with a resultant increased risk of myocardial infarction. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr22:37,966,253-37,976,024 Size: 9,772 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr22:37,966,270-37,975,912 Size: 9,643 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:37,966,253-37,976,024)mRNA (may differ from genome)Protein (132 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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MGIneXtProtOMIMPubMedTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LEG2_HUMAN
DESCRIPTION: RecName: Full=Galectin-2; Short=Gal-2; AltName: Full=Beta-galactoside-binding lectin L-14-II; AltName: Full=HL14; AltName: Full=Lactose-binding lectin 2; AltName: Full=S-Lac lectin 2;
FUNCTION: This protein binds beta-galactoside. Its physiological function is not yet known.
SUBUNIT: Homodimer.
SIMILARITY: Contains 1 galectin domain.
WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=Galectin-2; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Stlect_280";

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LGALS2
CDC HuGE Published Literature: LGALS2
Positive Disease Associations: Antidepressive Agents , myocardial infarct , Myocardial Infarction
Related Studies:
  1. Antidepressive Agents
    S L Clark et al. Psychological medicine 2012, Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D., Psychological medicine. [PubMed 22041458]
    Although our findings require replication and functional validation, this study demonstrates the potential of GWAS to discover genes and pathways that could mediate adverse effects of antidepressant medication.
  2. myocardial infarct
    Koch, W. et al. 2007, Association of variants in the BAT1-NFKBIL1-LTA genomic region with protection against myocardial infarction in Europeans, Hum Mol Genet 2007. [PubMed 17517687]
  3. Myocardial Infarction
    Ozaki K 2004, Functional variation in LGALS2 confers risk of myocardial infarction and regulates lymphotoxin-alpha secretion in vitro., Nature. 2004 May;429(6987):72-5. [PubMed 15129282]
    Our findings thus suggest a link between the LTA cascade and the pathogenesis of MI.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: LGALS2
Diseases sorted by gene-association score: myocardial infarction* (242)
* = 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: 49.28 RPKM in Small Intestine - Terminal Ileum
Total median expression: 131.34 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 -31.00112-0.277 Picture PostScript Text
3' UTR 0.00170.000 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
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR001079 - Galectin_CRD

Pfam Domains:
PF00337 - Galactoside-binding lectin

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1HLC - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P05162
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016936 galactoside binding
GO:0030246 carbohydrate binding


-  Descriptions from all associated GenBank mRNAs
  BC029063 - Homo sapiens lectin, galactoside-binding, soluble, 2, mRNA (cDNA clone IMAGE:5189510), partial cds.
BC059782 - Homo sapiens lectin, galactoside-binding, soluble, 2, mRNA (cDNA clone MGC:75071 IMAGE:5185491), complete cds.
LP896262 - Sequence 1126 from Patent EP3253886.
M14079 - Human HL14 gene encoding beta-galactoside-binding lectin, 3' end, clone 1.
CR456512 - Homo sapiens LGALS2 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.LGALS2.V3).
M87842 - Human S-lac lectin L-14-II (LGALS2) mRNA, complete cds.
CR541972 - Homo sapiens full open reading frame cDNA clone RZPDo834E1234D for gene LGALS2, lectin, galactoside-binding, soluble, 2 (galectin 2); complete cds, incl. stopcodon.
CU013111 - Homo sapiens LGALS2, mRNA (cDNA clone IMAGE:100000369), complete cds, with stop codon, in Gateway system.
KJ891543 - Synthetic construct Homo sapiens clone ccsbBroadEn_00937 LGALS2 gene, encodes complete protein.
CR542000 - Homo sapiens full open reading frame cDNA clone RZPDo834A1235D for gene LGALS2, lectin, galactoside-binding, soluble, 2 (galectin 2); complete cds, without stopcodon.
CU013399 - Homo sapiens LGALS2, mRNA (cDNA clone IMAGE:100000273), complete cds, without stop codon, in Gateway system.
CU687384 - Synthetic construct Homo sapiens gateway clone IMAGE:100021547 5' read LGALS2 mRNA.
JD200335 - Sequence 181359 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: LEG2_HUMAN, NM_006498, NP_006489, P05162, Q6FGY4
UCSC ID: uc003ata.3
RefSeq Accession: NM_006498
Protein: P05162 (aka LEG2_HUMAN)
CCDS: CCDS13950.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006498.2
exon count: 4CDS single in 3' UTR: no RNA size: 543
ORF size: 399CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 974.00frame shift in genome: no % Coverage: 97.24
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.