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CHI3L2 Gene

protein-coding   GIFtS: 56
GCID: GC01P111770

Chitinase 3-Like 2

  Search for CHI3L2
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chitinase 3-Like 21 2
Chondrocyte Protein 392 3
YKL-392 3
YKL392 5
CHIL22
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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CHI3L2 Gene:
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)

GeneCards Summary for CHI3L2 Gene:
CHI3L2 (chitinase 3-like 2) is a protein-coding gene. GO annotations related to this gene include chitin binding and chitinase activity. An important paralog of this gene is CHI3L1.

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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_032977.10  
Regulatory elements:
   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 Chromatin IP Primers for CHI3L2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CH3L2_HUMAN, Q15782 (See protein sequence)
Recommended Name: Chitinase-3-like protein 2 precursor  
Size: 390 amino acids; 43501 Da
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: A6NNY3 B4DPR7 Q15749 Q15783 Q5VUV7 Q96F97
Alternative splicing: 3 isoforms:  Q15782-4   Q15782-5   Q15782-6   

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

Explore proteomics data for CHI3L2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys199, Lys329, Lys340, Lys345, Lys384
  • Glycosylation2 at Asn35
  • Modification sites at PhosphoSitePlus

  • See CHI3L2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    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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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    5 InterPro protein domains:
     IPR011583 Chitinase_II
     IPR028541 CHI3L2
     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 domains:
    IPB001223 Glycoside hydrolase
    IPB001579 Glycoside hydrolase
    IPB011583 Chitinase II


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


    Find genes that share domains with CHI3L2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: 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

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds ----
    GO:0004568NOT chitinase activity IDA--
    GO:0008061chitin binding IDA--
         
    Find genes that share ontologies with CHI3L2           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CHI3L2
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    miRTarBase miRNAs that target CHI3L2:
    hsa-mir-335-5p (MIRT018662)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CH3L2_HUMAN, Q15782: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular4
    golgi apparatus1
    mitochondrion1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--

    Find genes that share ontologies with CHI3L2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CHI3L2
    Interactions:

        Search GeneGlobe Interaction Network for CHI3L2

    Gene Ontology (GO): 2 biological process terms:    About this table

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

    Find genes that share ontologies with CHI3L2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CHI3L2 (CH3L2)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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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      QuantiTect SYBR Green Assays in human, mouse, rat CHI3L2
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    Additional mRNA 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 

    Selected AceView cDNA sequences (see all 314):

    CR623620 AA297691 BU180840 AA130212 BM835326 BM709168 AA312670 BF725041 
    BF798019 CR603396 BG698401 AL598808 BU753932 U58514 BF663177 BQ054482 
    AI472612 CR597779 BM835429 AW292283 CR610069 CR625467 BQ013485 BQ059746 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CHI3L2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGGATTCCC
    CHI3L2 Expression
    About this image


    CHI3L2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Bone (Muscoskeletal System)
             Articular chondrocyte-like cells
     
     Cartilage (Muscoskeletal System)
             Articular chondrocyte-like cells
     
     Adipose (Muscoskeletal System)    fully expand to see all 2 entries
             White adipocyte-like cells
     
     Thymus (Hematopoietic System)
             Double Positive Thymocytes Thymus
     
     Neural Crest (Gastrulation Derivatives)
             PureStem SK11, NCr-fac & Meso-prx Progenitor
    CHI3L2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CHI3L2 Protein Expression

    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)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for CHI3L2 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    oppossum
    (Monodelphis domestica)
    Mammalia CHI3L26
    chitinase 3-like 2
    62(a)
    1 ↔ 1
    2(481121540-481137153)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    48(a)
    45(a)
    1 ↔ many
    1 ↔ many
    4(119000203-119017951)
    4(118973309-118986277)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG29893 chitinase 40(a)
    (best of 9)
      9A4   --
    worm
    (Caenorhabditis elegans)
    Secernentea cht-16
    Protein CHT-1 (cht-1) mRNA, complete cds
    24(a)
    1 → many
    X(3397608-3400017) WBGene00000503
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes CTS26
    Putative chitinase, functionally complements A. go...
    19(a)
    1 → many
    IV(1219413-1220948) YDR371W


    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)
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    Paralogs for CHI3L2 gene
    CHI3L12  CHIA2  CHIT12  OVGP12  
    5 SIMAP similar genes for CHI3L2 using alignment to 10 protein entries:     CH3L2_HUMAN (see all proteins):
    CHI3L1    CHIA    CHIT1    FLJ00314    OVGP1

    Find genes that share paralogs with CHI3L2           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for CHI3L2
    PGOHUM00000258092


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CHI3L2 (see all 503)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs789355101,2
    C,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,F--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
         Database of Genomic Variants (DGV) 2 variations for CHI3L2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv463250CNV Loss19166990
    nsv10639CNV Gain18304495

    Human Gene Mutation Database (HGMD): CHI3L2
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CHI3L2
    DNA2.0 Custom Variant and Variant Library Synthesis for CHI3L2

    (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.)
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    OMIM gene information: 601526    OMIM disorders: --


    Find genes that share disorders with CHI3L2           About GenesLikeMe

    Genetic Association Database (GAD): CHI3L2
    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)
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    PubMed articles for CHI3L2 gene, integrated from 10 sources (see all 23):
    (articles sorted by number of sources associating them with CHI3L2)
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    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. (J. Biol. Chem. 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. (Biochem. J. 2012)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    4. 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. (Biochem. Biophys. Res. Commun. 2002)
    5. Human YKL39 (chitinase 3-like protein 2), an osteoarthritis-associated gene, enhances proliferation and type II collagen expression in ATDC5 cells. (PubMed id 23291184)1 Miyatake K....Muneta T. (Biochem. Biophys. Res. Commun. 2013)
    6. New paralogues and revised time line in the expansion of the vertebrate GH18 family. (PubMed id 23558346)1 Hussain M. and Wilson J.B. (J. Mol. Evol. 2013)
    7. Two closely related human members of chitinase-like family, CHI3L1 and CHI3L2, activate ERK1/2 in 293 and U373 cells but have the different influence on cell proliferation. (PubMed id 22211103)1 Areshkov P.O....Kavsan V.M. (Int. J. Biol. Sci. 2012)
    8. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 JAoger S....Krogan N.J. (Nature 2012)
    9. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    10. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1117 HGNC: 1933 AceView: CHI3L2 Ensembl:ENSG00000064886 euGenes: HUgn1117
    ECgene: CHI3L2 H-InvDB: CHI3L2

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    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:
    Search GeneIP for patents involving CHI3L2

    GeneCards and IP:
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