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Clvs1 clavesin 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 366311, updated on 17-Aug-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, Apr 2022]
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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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 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

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