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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CHI3L2 Gene

protein-coding   GIFtS: 52
GCID: GC01P111770

chitinase 3-like 2

 Explore 5 diseases affiliated with
CHI3L2 via our new
 Human Malady Compendium 
Biological research products
for CHI3L2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Chitinase 3-Like 21 2
YKL-391 2 3
YKL391 2
Chondrocyte Protein 392 3
Chitinase-3-Like Protein 22

External Ids:    HGNC: 19331   Entrez Gene: 11172   Ensembl: ENSG000000648867   OMIM: 6015265   UniProtKB: Q157823   

Export aliases for CHI3L2 gene to outside databases

Previous GC identifers: GC01P112186 GC01P110642 GC01P110872 GC01P111069 GC01P111482 GC01P111571 GC01P109641


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CHI3L2:
The protein encoded by this gene is similar to bacterial chitinases but lacks chitinase activity. The encoded protein
is secreted and is involved in cartilage biogenesis. Several transcript variants encoding different isoforms have been
found for this gene. (provided by RefSeq, Apr 2012)

UniProtKB/Swiss-Prot: CH3L2_HUMAN, Q15782
Function: Lectin that binds chitooligosaccharides and other glycans with high affinity, but not heparin. Has no
chitinase activity




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CHI3L2 gene promoter:
         AML1a   Tal-1   LCR-F1   Ik-3   NF-AT   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCHI3L2 promoter sequence
   Search SABiosciences Chromatin IP Primers for CHI3L2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CHI3L2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p13.3   Ensembl cytogenetic band:  1p13.3   HGNC cytogenetic band: 1p13.3

CHI3L2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CHI3L2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P111770:  view genomic region     (about GC identifiers)

Start:
111,743,393 bp from pter      End:
111,786,062 bp from pter
Size:
42,670 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CH3L2_HUMAN, Q15782 (See protein sequence)
Recommended Name: Chitinase-3-like protein 2 precursor  
Size: 390 amino acids; 43501 Da
Subcellular location: Secreted (Potential)
Caution: Lacks the conserved sequence motif DxxDxDxE that is essential for the catalytic activity of chitinases of the
glycosyl hydrolase 18 family, and therefore has no chitinase activity
Sequence caution: Sequence=AAB04534.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=AAC50597.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
1 PDB 3D structure from and Proteopedia for CHI3L2:
4AY1 (3D)    
Secondary accessions: B4DPR7 Q15749 Q15783 Q5VUV7 Q96F97
Alternative splicing: 2 isoforms:  Q15782-4   Q15782-5   

Explore the universe of human proteins at neXtProt for CHI3L2: NX_Q15782

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q15782

  • CHI3L2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001020368.1  NP_001020370.1  NP_003991.2  

    ENSEMBL proteins: 
     ENSP00000437082   ENSP00000436077   ENSP00000431968   ENSP00000358759   ENSP00000436380  
     ENSP00000437086   ENSP00000436272   ENSP00000431978   ENSP00000436006   ENSP00000432049  
     ENSP00000433176   ENSP00000435250   ENSP00000435935   ENSP00000358763  

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    Uscn Proteins for CHI3L2

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space TAS8702629


    CHI3L2 for ontologies           About GeneDecksing



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

    CHI3L2 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR011583 Chitinase_II
     IPR017853 Glycoside_hydrolase_SF
     IPR001223 Glyco_hydro18cat
     IPR013781 Glyco_hydro_catalytic_dom

    Graphical View of Domain Structure for InterPro Entry Q15782

    ProtoNet protein and cluster: Q15782

    3 Blocks protein families:
    IPB001223 Glycoside hydrolase
    IPB001579 Glycoside hydrolase
    IPB011583 Chitinase II


    UniProtKB/Swiss-Prot: CH3L2_HUMAN, Q15782
    Similarity: Belongs to the glycosyl hydrolase 18 family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CH3L2_HUMAN, Q15782
    Function: Lectin that binds chitooligosaccharides and other glycans with high affinity, but not heparin. Has no
    chitinase activity

         Genatlas biochemistry entry for CHI3L2:
    chitinase 3-like 2,expressed in chondrocytes,synovial cell,lung,heart

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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds ----
    GO:0004568NOT chitinase activity IDA--
    GO:0008061chitin binding IDA--
    GO:0043169cation binding IEA--


    CHI3L2 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CHI3L2

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005975carbohydrate metabolic process IEA--
    GO:0006032chitin catabolic process IEA--


    CHI3L2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CHI3L2
    Search CenterWatch for drugs/clinical trials and news about CHI3L2 / CH3L2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CHI3L2 gene (3 alternative transcripts): 
    NM_001025197.1  NM_001025199.1  NM_004000.2  

    Unigene Cluster for CHI3L2:

    Chitinase 3-like 2
    Hs.514840  [show with all ESTs]
    Unigene Representative Sequence: NM_001025199
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000445067(uc001eam.3) ENST00000528451 ENST00000486561 ENST00000369744(uc001ean.3)
    ENST00000474304 ENST00000466741(uc001eao.3) ENST00000477185 ENST00000467038
    ENST00000497587 ENST00000526684 ENST00000530597 ENST00000524472 ENST00000533831
    ENST00000497220 ENST00000472825 ENST00000529459 ENST00000369748

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    Additional cDNA sequence: 

    AK223316.1 AK298466.1 BC011460.1 BT006767.1 U49835.1 U58514.1 U58515.1 

    14 DOTS entries:

    DT.100781460  DT.444662  DT.92431814  DT.91906248  DT.92431820  DT.121409362  DT.92431815  DT.100781457 
    DT.121409386  DT.121409389  DT.121409455  DT.99948588  DT.99950230  DT.91730060 

    24/314 AceView cDNA sequences (see all 314):

    BG698401 BU180840 BQ054482 AI472612 CR626113 AA305977 BX415038 BF725041 
    BF663177 AA130212 BQ050325 CR623620 BX284062 AA297691 AL598808 BQ013485 
    BM835429 BM818103 BM789158 BM704964 BP367646 BM835326 CR603396 AA312670 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CHI3L2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGGGATTCCC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    CHI3L2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    PureStem™ mesenchymal Progenitor SK11 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    Articular chondrocyte-like cells (HyStem chondrogenic ...)Cartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CHI3L2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CHI3L2

    SOURCE GeneReport for Unigene cluster: Hs.514840

    UniProtKB/Swiss-Prot: CH3L2_HUMAN, Q15782
    Tissue specificity: Highest expression in chondrocytes, followed by synoviocytes, lung and heart. Not detected in
    spleen, pancreas, and liver. May also be expressed in developing brain and placenta

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for CHI3L2 gene from 5/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia CHI3L26
    --
    48(a)
    1 ↔ 1
    4(119001896-119016512)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG29893 chitinase 40(a)
    (best of 9)
      9A4   --
    worm
    (Caenorhabditis elegans)
    Secernentea F15A4.86
    T01C4.16
    (see all 31)
    Protein T01C4.1
    (see all 31)
    8(a)
    5(a)
    (see all 31)
    possible ortholog
    possible ortholog
    (see all 31)
    II(12475274-12478862)
    V(7123639-7128871)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G197706
    AT4G198206
    (see all 9)
    Glycosyl hydrolase family protein with chitinase i...
    Glycosyl hydrolase family protein with chitinase i...
    (see all 9)
    28(a)
    27(a)
    (see all 9)
    many ↔ many
    many ↔ many
    (see all 9)
    4(10753310-10754181)
    4(10767436-10768614)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    glycosyl hydrolase, putative, expressed
    21(a)
    19(a)
    many ↔ many
    many ↔ many
    11(15300987-15302654)
    4(18220682-18222511)


    ENSEMBL Gene Tree for CHI3L2 (if available)
    TreeFam Gene Tree for CHI3L2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CHI3L2 gene
    CHI3L12  CHIA2  CHIT12  OVGP12  
    5 SIMAP similar genes for CHI3L2 using alignment to 11 protein entries:     CH3L2_HUMAN (see all proteins):
    CHI3L1    CHIT1    CHIA    FLJ00314    OVGP1

    CHI3L2 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CHI3L2
    PGOHUM00000258092


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/402 NCBI SNPs in CHI3L2 are shown (see all 402    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs789355101,2
    F,--111768385(+) AAGTAC/TGGAGA 2 -- us2k11Minor allele frequency- T:0.04WA 118
    rs1475529961,2
    --111768422(+) AGAGCA/GAATGC 2 -- us2k10--------
    rs1490384651,2
    --111768446(+) GAAATA/GCTACA 2 -- us2k10--------
    rs1811322131,2
    --111768460(+) ACCTTC/GTTCAG 2 -- us2k10--------
    rs31182071,2
    C,F,A,H,--111768576(-) CAGAGC/TGAGAC 2 -- us2k18Minor allele frequency- T:0.23NA WA EA 254
    rs346878791,2
    C,F,--111768619(+) ACCTCA/GTTTTA 2 -- us2k15Minor allele frequency- G:0.16NA WA EA 362
    rs1854391621,2
    --111768621(+) CTCATG/TTTAAA 2 -- us2k10--------
    rs347726141,2
    C,--111768746(+) GCTGAG/AGTATT 2 -- us2k13Minor allele frequency- A:0.14NA EA 242
    rs1124950411,2
    C,F,--111768817(+) CAGCTG/ATAACA 2 -- us2k14Minor allele frequency- A:0.06NA CSA WA 242
    rs1145570491,2
    F,--111768855(+) ACAAAC/TGTCTA 2 -- us2k11Minor allele frequency- T:0.03WA 118

    HapMap Linkage Disequilibrium report for CHI3L2 (111743393 - 111786062 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for CHI3L2
         1 CNV: 30401
    Human Gene Mutation Database (HGMD): CHI3L2

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    CHI3L2 for disorders           About GeneDecksing

    OMIM gene information: 601526    OMIM disorders: --

    5 diseases for CHI3L2:    About MalaCards
    chitotriosidase deficiency    rheumatoid arthritis    arthritis    osteoarthritis
    glioblastoma

    Human Genome Epidemiology (HuGE) Navigator: CHI3L2 (1 document)

    Export disorders for CHI3L2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CHI3L2 gene, integrated from 9 sources (see all 19):
    (articles sorted by number of sources associating them with CHI3L2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and sequence of a novel human chondrocyte protein related to mammalian members of the chitinase protein family. (PubMed id 8702629)1, 2, 3, 9 Hu B.... Price P.A. (1996)
    2. Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties. (PubMed id 22742450)1, 2 Schimpl M....van Aalten D.M. (2012)
    3. Enhanced expression of the human chitinase 3-like 2 gene (YKL-39) but not chitinase 3-like 1 gene (YKL-40) in osteoarthritic cartilage. (PubMed id 12435396)1, 9 Steck E....Richter W. (2002)
    4. Two closely related human members of chitinase-like fa mily, CHI3L1 and CHI3L2, activate ERK1/2 in 293 and U373 cells but have the diff erent influence on cell proliferation. (PubMed id 22211103)1 Areshkov P.O....Kavsan V.M. (2012)
    5. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    7. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    8. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (2006)
    9. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 1117 HGNC: 1933 AceView: CHI3L2 Ensembl:ENSG00000064886 euGenes: HUgn1117
    ECgene: CHI3L2 H-InvDB: CHI3L2

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CHI3L2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CHI3L2 gene:
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