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    Chid1 chitinase domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 293628, updated on 13-Apr-2024

    Summary

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    Symbol
    Chid1provided by RGD
    Full Name
    chitinase domain containing 1provided by RGD
    Primary source
    RGD:1308955
    See related
    Ensembl:ENSRNOG00000063613 AllianceGenome:RGD:1308955
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Cc1-9; RGD1308955
    Summary
    Predicted to enable oligosaccharide binding activity. Predicted to be involved in negative regulation of cytokine production involved in inflammatory response. Predicted to be located in several cellular components, including late endosome; lysosome; and trans-Golgi network. Predicted to be active in extracellular region. Orthologous to human CHID1 (chitinase domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 102.2), Liver (RPKM 97.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    1q41
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (206024059..206059259, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (196594357..196629700, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (214476418..214511569, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene RNA polymerase II, I and III subunit L Neighboring gene tetraspanin 4 Neighboring gene RNA, U6 small nuclear 317 Neighboring gene adaptor related protein complex 2 subunit alpha 2 Neighboring gene uncharacterized LOC120097363

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Structure of human stabilin-1 interacting chitinase-like protein (SI-CLP) reveals a saccharide-binding cleft with lower sugar-binding selectivity. Meng G, et al. J Biol Chem, 2010 Dec 17. PMID 20724479, Free PMC Article
    2. Novel stabilin-1 interacting chitinase-like protein (SI-CLP) is up-regulated in alternatively activated macrophages and secreted via lysosomal pathway. Kzhyshkowska J, et al. Blood, 2006 Apr 15. PMID 16357325
    3. New paralogues and revised time line in the expansion of the vertebrate GH18 family. Hussain M, et al. J Mol Evol, 2013 Apr. PMID 23558346
    4. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). Gonzalez-Begne M, et al. J Proteome Res, 2009 Mar. PMID 19199708, Free PMC Article
    5. Proteomic characterization of the human sperm nucleus. de Mateo S, et al. Proteomics, 2011 Jul. PMID 21630459

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC156830

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chitin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oligosaccharide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables oligosaccharide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oligosaccharide binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cytokine production involved in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cytokine production involved in inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endomembrane system IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    chitinase domain-containing protein 1
    Names
    chitinase domain-containing protein 1-like
    NP_001041319.2
    NP_001408228.1
    NP_001408229.1
    XP_038963991.1
    XP_063142707.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001047854.3 → NP_001041319.2  chitinase domain-containing protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001041319.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      A0JPQ9
      UniProtKB/TrEMBL
      A6HY14
      Related
      ENSRNOP00000026390.7, ENSRNOT00000026390.8
      Conserved Domains (2) summary
      cd02876
      Location:80 → 396
      GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...
      smart00636
      Location:83 → 387
      Glyco_18; Glyco_18 domain

    2. NM_001421299.1 → NP_001408228.1  chitinase domain-containing protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A6HY14

    3. NM_001421300.1 → NP_001408229.1  chitinase domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      206024059..206059259 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039108063.2 → XP_038963991.1  chitinase domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      A0JPQ9
      Conserved Domains (1) summary
      cd02876
      Location:94 → 410
      GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

    2. XM_063286637.1 → XP_063142707.1  chitinase domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A140TAD5

    RNA

    1. XR_010065697.1 RNA Sequence

    2. XR_590539.4 RNA Sequence

    3. XR_010065698.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0JPQ9.2 GenPept UniProtKB/Swiss-Prot:A0JPQ9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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