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    Cltc clathrin heavy chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 54241, updated on 27-Nov-2024

    Summary

    Official Symbol
    Cltcprovided by RGD
    Official Full Name
    clathrin heavy chainprovided by RGD
    Primary source
    RGD:2364
    See related
    EnsemblRapid:ENSRNOG00000004291 AllianceGenome:RGD:2364
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables several functions, including ankyrin binding activity; heat shock protein binding activity; and protein serine/threonine kinase binding activity. Involved in Golgi organization; endocytosis; and mitotic cell cycle. Located in T-tubule and spindle. Part of clathrin coat. Is extrinsic component of synaptic vesicle membrane. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 56. Orthologous to human CLTC (clathrin heavy chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 1547.0), Brain (RPKM 1139.6) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Cltc in Genome Data Viewer
    Location:
    10q26
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (72014984..72073308, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (71517661..71574591, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (74014560..74070578, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene vacuole membrane protein 1 Neighboring gene peptidyl-tRNA hydrolase 2 Neighboring gene DEAH-box helicase 40 Neighboring gene uncharacterized LOC120095163

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ankyrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables clathrin light chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables clathrin light chain binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables clathrin light chain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables disordered domain specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables disordered domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables double-stranded RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables double-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables heat shock protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables low-density lipoprotein particle receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables low-density lipoprotein particle receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables peptide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein serine/threonine kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin-specific protease binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin-specific protease binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in amyloid-beta clearance by transcytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in amyloid-beta clearance by transcytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in clathrin coat assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in clathrin coat assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in clathrin coat assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in clathrin coat disassembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in clathrin-dependent endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in clathrin-dependent endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitotic cell cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within mitotic spindle assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of hyaluronan biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of hyaluronan biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of hyaluronan biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of protein localization to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of protein localization to plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in receptor internalization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in receptor internalization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in receptor-mediated endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in receptor-mediated endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of mitotic spindle organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of mitotic spindle organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in retrograde transport, endosome to Golgi IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptic vesicle endocytosis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in synaptic vesicle endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in transferrin transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transferrin transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of Myb complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in T-tubule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of clathrin coat IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of clathrin coat ISO
    Inferred from Sequence Orthology
    more info
     
    part_of clathrin coat TAS
    Traceable Author Statement
    more info
    PubMed 
    part_of clathrin coat of coated pit IEA
    Inferred from Electronic Annotation
    more info
     
    part_of clathrin coat of trans-Golgi network vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    part_of clathrin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of clathrin complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of clathrin complex ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in clathrin-coated endocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in clathrin-coated pit ISO
    Inferred from Sequence Orthology
    more info
     
    located_in clathrin-coated vesicle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in extrinsic component of synaptic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in glutamatergic synapse 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 melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
     
    part_of membrane coat ISO
    Inferred from Sequence Orthology
    more info
     
    located_in mitotic spindle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in mitotic spindle microtubule IEA
    Inferred from Electronic Annotation
    more info
     
    located_in mitotic spindle microtubule ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in photoreceptor ribbon synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in postsynaptic endocytic zone ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in presynaptic endocytic zone membrane ISO
    Inferred from Sequence Orthology
    more info
     
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in sarcolemma IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in spindle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in spindle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in spindle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in terminal bouton HDA PubMed 

    General protein information

    Preferred Names
    clathrin heavy chain 1
    Names
    clathrin, heavy chain (Hc)
    clathrin, heavy polypeptide (Hc)

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_019299.2NP_062172.2  clathrin heavy chain 1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/Swiss-Prot
      P11442
      Related
      ENSRNOP00000086473.2, ENSRNOT00000111406.2
      Conserved Domains (6) summary
      smart00299
      Location:12741416
      CLH; Clathrin heavy chain repeat homology
      sd00006
      Location:11051131
      TPR; TPR repeat [structural motif]
      pfam00637
      Location:9791119
      Clathrin; Region in Clathrin and VPS
      pfam01394
      Location:198234
      Clathrin_propel; Clathrin propeller repeat
      pfam09268
      Location:331354
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:356421
      Clathrin_H_link; Clathrin-H-link

    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_086028.1 Reference GRCr8

      Range
      72014984..72073308 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006247108.5XP_006247170.1  clathrin heavy chain 1 isoform X1

      UniProtKB/Swiss-Prot
      P11442
      Related
      ENSRNOP00000094065.2, ENSRNOT00000096168.2
      Conserved Domains (6) summary
      smart00299
      Location:12741416
      CLH; Clathrin heavy chain repeat homology
      sd00006
      Location:11051131
      TPR; TPR repeat [structural motif]
      pfam00637
      Location:9791119
      Clathrin; Region in Clathrin and VPS
      pfam01394
      Location:198234
      Clathrin_propel; Clathrin propeller repeat
      pfam09268
      Location:331354
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:356421
      Clathrin_H_link; Clathrin-H-link
    2. XM_063269684.1XP_063125754.1  clathrin heavy chain 1 isoform X3

    3. XM_063269683.1XP_063125753.1  clathrin heavy chain 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AGZ0
      Related
      ENSRNOP00000112235.1, ENSRNOT00000153028.1