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    Clvs1 clavesin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 366311, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Clvs1provided by RGD
    Official Full Name
    clavesin 1provided by RGD
    Primary source
    RGD:1564200
    See related
    EnsemblRapid:ENSRNOG00000006919 AllianceGenome:RGD:1564200
    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
    Rlbp1l1; Clavesin-1; RGD1564200
    Summary
    Predicted to enable phosphatidylinositol-3,5-bisphosphate binding activity. Involved in lysosome organization. Located in clathrin-coated vesicle and trans-Golgi network. Orthologous to human CLVS1 (clavesin 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 75.8), Heart (RPKM 39.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Clvs1 in Genome Data Viewer
    Location:
    5q13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (27107255..27401649)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (22408384..22604281)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (22380318..22580391)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108350931 Neighboring gene uncharacterized LOC134486919 Neighboring gene uncharacterized LOC134486918 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC134486920 Neighboring gene uncharacterized LOC120102822 Neighboring gene aspartate-beta-hydroxylase Neighboring gene uncharacterized LOC120102823

    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. The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. Katoh Y, et al. J Biol Chem, 2009 Oct 2. PMID 19651769, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in lysosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lysosome organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in clathrin-coated vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    clavesin-1
    Names
    Retinaldehyde-binding protein 1-like protein 1
    retinaldehyde-binding protein 1-like 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_001108969.2 → NP_001102439.1  clavesin-1

      See identical proteins and their annotated locations for NP_001102439.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/Swiss-Prot
      A6JFQ6
      UniProtKB/TrEMBL
      A6JFQ7, F1LRF3
      Related
      ENSRNOP00000009744.6, ENSRNOT00000009744.7
      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain

    2. NM_001428688.1 → NP_001415617.1  clavesin-1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/Swiss-Prot
      A6JFQ6
      UniProtKB/TrEMBL
      A6JFQ7, F1LRF3

    3. NM_001428689.1 → NP_001415618.1  clavesin-1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/Swiss-Prot
      A6JFQ6
      UniProtKB/TrEMBL
      A6JFQ7, F1LRF3

    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_086023.1 Reference GRCr8

      Range
      27107255..27401649
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063288103.1 → XP_063144173.1  clavesin-1 isoform X1

    2. XM_063288101.1 → XP_063144171.1  clavesin-1 isoform X1

    3. XM_063288104.1 → XP_063144174.1  clavesin-1 isoform X1

    4. XM_063288102.1 → XP_063144172.1  clavesin-1 isoform X1

    5. XM_017593530.3 → XP_017449019.2  clavesin-1 isoform X1

      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain

    6. XM_017593531.3 → XP_017449020.2  clavesin-1 isoform X1

      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6JFQ6.1 GenPept UniProtKB/Swiss-Prot:A6JFQ6

    Gene LinkOut

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