U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Fyco1 FYVE and coiled-coil domain autophagy adaptor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 301085, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Fyco1provided by RGD
    Official Full Name
    FYVE and coiled-coil domain autophagy adaptor 1provided by RGD
    Primary source
    RGD:1309069
    See related
    EnsemblRapid:ENSRNOG00000006336 AllianceGenome:RGD:1309069
    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
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in plus-end-directed vesicle transport along microtubule and positive regulation of autophagosome maturation. Predicted to be located in Golgi apparatus. Predicted to be active in autophagosome; late endosome; and lysosome. Human ortholog(s) of this gene implicated in cataract 18. Orthologous to human FYCO1 (FYVE and coiled-coil domain autophagy adaptor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 404.5), Muscle (RPKM 321.8) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Fyco1 in Genome Data Viewer
    Location:
    8q32
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (132289538..132356810, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (123412105..123479315, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (132844042..132910905, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene ribosomal biogenesis factor, pseudogene 1 Neighboring gene C-C motif chemokine receptor 9 Neighboring gene basic leucine zipper and W2 domains 1, pseudogene 2 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene X-C motif chemokine receptor 1 Neighboring gene CDK2-associated, cullin domain 1, pseudogene 1 Neighboring gene transcription initiation factor TFIID subunit 13-like

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. FYCO1 Contains a C-terminally Extended, LC3A/B-preferring LC3-interacting Region (LIR) Motif Required for Efficient Maturation of Autophagosomes during Basal Autophagy. Olsvik HL, et al. J Biol Chem, 2015 Dec 4. PMID 26468287, Free PMC Article
    2. FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport. Pankiv S, et al. J Cell Biol, 2010 Jan 25. PMID 20100911, Free PMC Article
    3. Defining the membrane proteome of NK cells. Ghosh D, et al. J Mass Spectrom, 2010 Jan. PMID 19946888
    4. 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

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in plus-end-directed vesicle transport along microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in plus-end-directed vesicle transport along microtubule ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    FYVE and coiled-coil domain-containing protein 1
    Names
    FYVE and coiled-coil domain containing 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001106870.2 → NP_001100340.1  FYVE and coiled-coil domain-containing protein 1

      See identical proteins and their annotated locations for NP_001100340.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A0G2K6G5, A6I4C6, D3Z9D2
      Related
      ENSRNOP00000008630.5, ENSRNOT00000008630.8
      Conserved Domains (5) summary
      COG3096
      Location:237 → 519
      MukB; Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Escherichia coli str. K-12 substr. MG1655 [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:392 → 1117
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1144 → 1200
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1392 → 1437
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 164
      RUN; RUN domain

    2. NM_001433268.1 → NP_001420197.1  FYVE and coiled-coil domain-containing protein 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A0G2K6G5, A6I4C6, D3Z9D2

    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_086026.1 Reference GRCr8

      Range
      132289538..132356810 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039081318.2 → XP_038937246.1  FYVE and coiled-coil domain-containing protein 1 isoform X1

      Related
      ENSRNOP00000073803.2, ENSRNOT00000087799.3
      Conserved Domains (5) summary
      COG3096
      Location:237 → 519
      MukB; Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Escherichia coli str. K-12 substr. MG1655 [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:392 → 1117
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1144 → 1200
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1392 → 1437
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 164
      RUN; RUN domain

    2. XM_017595602.3 → XP_017451091.1  FYVE and coiled-coil domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K6G5, A6I4C6, D3Z9D2
      Conserved Domains (5) summary
      COG3096
      Location:237 → 519
      MukB; Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Escherichia coli str. K-12 substr. MG1655 [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:392 → 1117
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1144 → 1200
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1392 → 1437
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 164
      RUN; RUN domain
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools