Human Gene CHI3L2 (ENST00000369748.9_7) from GENCODE V47lift37
  Description: chitinase 3 like 2, transcript variant 1 (from RefSeq NM_004000.3)
Gencode Transcript: ENST00000369748.9_7
Gencode Gene: ENSG00000064886.14_13
Transcript (Including UTRs)
   Position: hg19 chr1:111,770,335-111,786,062 Size: 15,728 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:111,770,352-111,784,986 Size: 14,635 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:111,770,335-111,786,062)mRNA (may differ from genome)Protein (390 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CH3L2_HUMAN
DESCRIPTION: RecName: Full=Chitinase-3-like protein 2; AltName: Full=Chondrocyte protein 39; AltName: Full=YKL-39; Flags: Precursor;
FUNCTION: Lectin that binds chitooligosaccharides and other glycans with high affinity, but not heparin. Has no chitinase activity.
SUBCELLULAR LOCATION: Secreted (Potential).
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.
SIMILARITY: Belongs to the glycosyl hydrolase 18 family.
CAUTION: Lacks the conserved sequence motif DxxDxDxE that is essential for the catalytic activity of chitinases of the glycosyl hydrolase 18 family, and 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;

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 56.14 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 153.59 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 0.00170.000 Picture PostScript Text
3' UTR -56.70226-0.251 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
IPR011583 - Chitinase_II
IPR001223 - Glyco_hydro18cat
IPR013781 - Glyco_hydro_catalytic_dom
IPR017853 - Glycoside_hydrolase_SF

Pfam Domains:
PF00704 - Glycosyl hydrolases family 18

SCOP Domains:
51445 - (Trans)glycosidases
54556 - Chitinase insertion domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
4AY1 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15782
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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    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008061 chitin binding
GO:0016787 hydrolase activity
GO:0030246 carbohydrate binding
GO:0004568 chitinase activity

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0006032 chitin catabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  U58514 - Human chitinase precursor (HUMTCHIT) mRNA, exon 1a form, complete cds.
U49835 - Human YKL-39 precursor mRNA, complete cds.
BC011460 - Homo sapiens chitinase 3-like 2, mRNA (cDNA clone MGC:17183 IMAGE:4214121), complete cds.
KJ896599 - Synthetic construct Homo sapiens clone ccsbBroadEn_05993 CHI3L2 gene, encodes complete protein.
BT006767 - Homo sapiens chitinase 3-like 2 mRNA, complete cds.
DQ893705 - Synthetic construct Homo sapiens clone IMAGE:100008165; FLH163924.01L; RZPDo839A11161D chitinase 3-like 2 (CHI3L2) gene, encodes complete protein.
CU679936 - Synthetic construct Homo sapiens gateway clone IMAGE:100017158 5' read CHI3L2 mRNA.
U58515 - Human chitinase (HUMTCHIT) mRNA, exon 1b form, partial cds.
AK298466 - Homo sapiens cDNA FLJ57554 complete cds, highly similar to Chitinase 3-like protein 2 precursor.
AK223316 - Homo sapiens mRNA for chitinase 3-like 2 variant, clone: TMS08833.
JD431931 - Sequence 412955 from Patent EP1572962.
JD559439 - Sequence 540463 from Patent EP1572962.
JD537210 - Sequence 518234 from Patent EP1572962.
JD338915 - Sequence 319939 from Patent EP1572962.
JD342002 - Sequence 323026 from Patent EP1572962.
JD429405 - Sequence 410429 from Patent EP1572962.
JD551258 - Sequence 532282 from Patent EP1572962.
JD501407 - Sequence 482431 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NNY3, B4DPR7, CH3L2_HUMAN, ENST00000369748.1, ENST00000369748.2, ENST00000369748.3, ENST00000369748.4, ENST00000369748.5, ENST00000369748.6, ENST00000369748.7, ENST00000369748.8, NM_004000, Q15749, Q15782, Q15783, Q5VUV7, Q96F97, uc318huz.1, uc318huz.2
UCSC ID: ENST00000369748.9_7
RefSeq Accession: NM_004000.3
Protein: Q15782 (aka CH3L2_HUMAN or C3L2_HUMAN)

-  Gene Model Information
  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.