LOCUS       NM_004000               1416 bp    mRNA    linear   PRI 02-APR-2024
DEFINITION  Homo sapiens chitinase 3 like 2 (CHI3L2), transcript variant 1,
            mRNA.
ACCESSION   NM_004000
VERSION     NM_004000.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1416)
  AUTHORS   Qian,W., Wang,Q., Zhang,C., Zhu,J., Zhang,Q. and Luo,C.
  TITLE     M2 macrophage marker CHI3L2 could serve as a potential prognostic
            and immunological biomarker in glioma by integrated single-cell and
            bulk RNA-Seq analysis
  JOURNAL   J Gene Med 25 (9), e3523 (2023)
   PUBMED   37147894
  REMARK    GeneRIF: M2 macrophage marker CHI3L2 could serve as a potential
            prognostic and immunological biomarker in glioma by integrated
            single-cell and bulk RNA-Seq analysis.
REFERENCE   2  (bases 1 to 1416)
  AUTHORS   Nimbalkar,V.P., Kruthika,B.S., Sravya,P., Rao,S., Sugur,H.S.,
            Chickabasaviah,Y.T., Somanna,S., Arivazhagan,A., Kondaiah,P. and
            Santosh,V.
  TITLE     Chitinase 3-Like 2
  JOURNAL   Am J Clin Pathol 158 (4), 521-529 (2022)
   PUBMED   35913110
  REMARK    GeneRIF: Chitinase 3-Like 2.
REFERENCE   3  (bases 1 to 1416)
  AUTHORS   Ogunkolade,B.W., Adaikalakoteswari,A., Cardoso,S.R., Lowe,R.,
            Patel,N., Rakyan,V., Finer,S., Wabitsch,M., Saravanan,P.,
            Tripathi,G., Bochukova,E. and Hitman,G.A.
  TITLE     An integrative epi-transcriptomic approach identifies the human
            cartilage chitinase 3-like protein 2 (CHI3L2) as a potential
            mediator of B12 deficiency in adipocytes
  JOURNAL   Epigenetics 17 (10), 1219-1233 (2022)
   PUBMED   34818986
  REMARK    GeneRIF: An integrative epi-transcriptomic approach identifies the
            human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential
            mediator of B12 deficiency in adipocytes.
REFERENCE   4  (bases 1 to 1416)
  AUTHORS   Petrzalka,M., Meluzinova,E., Libertinova,J., Mojzisova,H.,
            Hanzalova,J., Rockova,P., Elisak,M., Kmetonyova,S., Sanda,J.,
            Sobek,O. and Marusic,P.
  TITLE     IL-2, IL-6 and chitinase 3-like 2 might predict early relapse
            activity in multiple sclerosis
  JOURNAL   PLoS One 17 (6), e0270607 (2022)
   PUBMED   35759479
  REMARK    GeneRIF: IL-2, IL-6 and chitinase 3-like 2 might predict early
            relapse activity in multiple sclerosis.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1416)
  AUTHORS   Li,H., Wang,D., Yi,B., Cai,H., Xi,Z., Lou,X. and Li,Z.
  TITLE     Comprehensive Analysis of CD163 as a Prognostic Biomarker and
            Associated with Immune Infiltration in Glioblastoma Multiforme
  JOURNAL   Biomed Res Int 2021, 8357585 (2021)
   PUBMED   34395626
  REMARK    GeneRIF: Comprehensive Analysis of CD163 as a Prognostic Biomarker
            and Associated with Immune Infiltration in Glioblastoma Multiforme.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1416)
  AUTHORS   Areshkov,P.O., Avdieiev,S.S., Balynska,O.V., Leroith,D. and
            Kavsan,V.M.
  TITLE     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
  JOURNAL   Int J Biol Sci 8 (1), 39-48 (2012)
   PUBMED   22211103
  REMARK    GeneRIF: ERK1/2 phosphorylation by CHI3L2 inhibits cell mitogenesis
            and proliferation.
REFERENCE   7  (bases 1 to 1416)
  AUTHORS   Palmer,D.J., Kelly,V.C., Smit,A.M., Kuy,S., Knight,C.G. and
            Cooper,G.J.
  TITLE     Human colostrum: identification of minor proteins in the aqueous
            phase by proteomics
  JOURNAL   Proteomics 6 (7), 2208-2216 (2006)
   PUBMED   16502470
REFERENCE   8  (bases 1 to 1416)
  AUTHORS   Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
            Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
            Kim,N.S.
  TITLE     Transcriptome analysis of human gastric cancer
  JOURNAL   Mamm Genome 16 (12), 942-954 (2005)
   PUBMED   16341674
REFERENCE   9  (bases 1 to 1416)
  AUTHORS   Steck,E., Breit,S., Breusch,S.J., Axt,M. and Richter,W.
  TITLE     Enhanced expression of the human chitinase 3-like 2 gene (YKL-39)
            but not chitinase 3-like 1 gene (YKL-40) in osteoarthritic
            cartilage
  JOURNAL   Biochem Biophys Res Commun 299 (1), 109-115 (2002)
   PUBMED   12435396
  REMARK    GeneRIF: human chitinase 3-like 2 gene (YKL-39) but not chitinase
            3-like 1 gene (YKL-40) is upregulated in osteoarthritic cartilage
REFERENCE   10 (bases 1 to 1416)
  AUTHORS   Hu,B., Trinh,K., Figueira,W.F. and Price,P.A.
  TITLE     Isolation and sequence of a novel human chondrocyte protein related
            to mammalian members of the chitinase protein family
  JOURNAL   J Biol Chem 271 (32), 19415-19420 (1996)
   PUBMED   8702629
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BG698401.1, U58514.1 and
            BQ181849.1.
            
            On Nov 22, 2018 this sequence version replaced NM_004000.2.
            
            Summary: 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].
            
            Transcript Variant: This variant (1) encodes the longest isoform
            (a).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR5189652.37185.1,
                                           SRR5189652.40748.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000369748.9/ ENSP00000358763.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-577               BG698401.1         55-631
            578-1415            U58514.1           597-1434
            1416-1416           BQ181849.1         17-17               c
FEATURES             Location/Qualifiers
     source          1..1416
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p13.2"
     gene            1..1416
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /note="chitinase 3 like 2"
                     /db_xref="GeneID:1117"
                     /db_xref="HGNC:HGNC:1933"
                     /db_xref="MIM:601526"
     exon            1..57
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     CDS             18..1190
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; chondrocyte protein 39; chitinase-3-like
                     protein 2"
                     /codon_start=1
                     /product="chitinase-3-like protein 2 isoform a precursor"
                     /protein_id="NP_003991.2"
                     /db_xref="CCDS:CCDS30802.1"
                     /db_xref="GeneID:1117"
                     /db_xref="HGNC:HGNC:1933"
                     /db_xref="MIM:601526"
                     /translation="MGATTMDQKSLWAGVVVLLLLQGGSAYKLVCYFTNWSQDRQEPG
                     KFTPENIDPFLCSHLIYSFASIENNKVIIKDKSEVMLYQTINSLKTKNPKLKILLSIG
                     GYLFGSKGFHPMVDSSTSRLEFINSIILFLRNHNFDGLDVSWIYPDQKENTHFTVLIH
                     ELAEAFQKDFTKSTKERLLLTAGVSAGRQMIDNSYQVEKLAKDLDFINLLSFDFHGSW
                     EKPLITGHNSPLSKGWQDRGPSSYYNVEYAVGYWIHKGMPSEKVVMGIPTYGHSFTLA
                     SAETTVGAPASGPGAAGPITESSGFLAYYEICQFLKGAKITRLQDQQVPYAVKGNQWV
                     GYDDVKSMETKVQFLKNLNLGGAMIWSIDMDDFTGKSCNQGPYPLVQAVKRSLGSL"
     exon            58..87
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            88..289
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            290..346
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            347..497
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            498..622
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            623..752
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            753..935
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            936..1052
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            1053..1192
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     exon            1193..1416
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1388..1393
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /note="hexamer: AATAAA"
     polyA_site      1416
                     /gene="CHI3L2"
                     /gene_synonym="CHIL2; YKL-39; YKL39"
                     /note="major polyA site"
ORIGIN      
        1 agaagctggc caaggatatg ggagcaacca ccatggacca gaagtctctc tgggcaggtg
       61 tagtggtctt gctgcttctc cagggaggat ctgcctacaa actggtttgc tactttacca
      121 actggtccca ggaccggcag gaaccaggaa aattcacccc tgagaatatt gaccccttcc
      181 tatgctctca tctcatctat tcattcgcca gcatcgaaaa caacaaggtt atcatcaagg
      241 acaagagtga agtgatgctc taccagacca tcaacagtct caaaaccaag aatcccaaac
      301 tgaaaattct cttgtccatt ggagggtacc tgtttggttc caaagggttc caccctatgg
      361 tggattcttc tacatcacgc ttggaattca ttaactccat aatcctgttt ctgaggaacc
      421 ataactttga tggactggat gtaagctgga tctacccaga tcagaaagaa aacactcatt
      481 tcactgtgct gattcatgag ttagcagaag cctttcagaa ggacttcaca aaatccacca
      541 aggaaaggct tctcttgact gcgggcgtat ctgcagggag gcaaatgatt gataacagct
      601 atcaagttga gaaactggca aaagatctgg atttcatcaa cctcctgtcc tttgacttcc
      661 atgggtcttg ggaaaagccc cttatcactg gccacaacag ccctctgagc aaggggtggc
      721 aggacagagg gccaagctcc tactacaatg tggaatatgc tgtggggtac tggatacata
      781 agggaatgcc atcagagaag gtggtcatgg gcatccccac atatgggcac tccttcacac
      841 tggcctctgc agaaaccacc gtgggggccc ctgcctctgg ccctggagct gctggaccca
      901 tcacagagtc ttcaggcttc ctggcctatt atgagatctg ccagttcctg aaaggagcca
      961 agatcacgcg gctccaggat cagcaggttc cctacgcagt caaggggaac cagtgggtgg
     1021 gctatgatga tgtgaagagt atggagacca aggttcagtt cttaaagaat ttaaacctgg
     1081 gaggagccat gatctggtct attgacatgg atgacttcac tggcaaatcc tgcaaccagg
     1141 gcccttaccc tcttgtccaa gcagtcaaga gaagccttgg ctccctgtga aggattaact
     1201 tacagagaag caggcaagat gaccttgctg cctggggcct gctctctccc aggaattctc
     1261 atgtgggatt ccccttgcca ggctggcctt tggatctctc ttccaagcct ttcctgactt
     1321 cctcttagat catagattgg acctggtttt gttttcctgc agctgttgac ttgttgccct
     1381 gaagtacaat aaaaaaaatt cattttgctc cagtaa
//
