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

Gene ID: 301085, updated on 2-Nov-2024

Summary

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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, Nov 2024]
Expression
Biased expression in Heart (RPKM 404.5), Muscle (RPKM 321.8) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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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

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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. 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

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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

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Preferred Names
FYVE and coiled-coil domain-containing protein 1
Names
FYVE and coiled-coil domain containing 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_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
    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

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