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    Phaf1 phagophore assembly factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 207123, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Phaf1provided by RGD
    Official Full Name
    phagophore assembly factor 1provided by RGD
    Primary source
    RGD:621098
    See related
    EnsemblRapid:ENSRNOG00000014668 AllianceGenome:RGD:621098
    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
    Lin10; Lin-10; RGD621098
    Summary
    Enables PDZ domain binding activity and glutamate receptor binding activity. Involved in Golgi to plasma membrane protein transport. Located in dendrite; synaptic vesicle membrane; and trans-Golgi network. Orthologous to human PHAF1 (phagosome assembly factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 149.8), Lung (RPKM 146.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phaf1 in Genome Data Viewer
    Location:
    19q11
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (50011350..50050880)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (33101453..33138920)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (37179850..37207714)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene core-binding factor subunit beta Neighboring gene ribosomal protein L27, pseudogene 10 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 Neighboring gene TNFRSF1A-associated via death domain Neighboring gene F-box and leucine-rich repeat protein 8 Neighboring gene heat shock transcription factor 4 Neighboring gene microtubule associated tyrosine carboxypeptidase 1 Neighboring gene nucleolar protein 3 Neighboring gene exocyst complex component 3-like 1

    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 PDZ domains of mLin-10 regulate its trans-Golgi network targeting and the surface expression of AMPA receptors. Stricker NL, et al. Neuropharmacology, 2003 Nov. PMID 14529721
    2. Molecular cloning and characterization of rat lin-10. Ide N, et al. Biochem Biophys Res Commun, 1998 Feb 13. PMID 9480860
    3. Interaction of rat lin-10 with brain-enriched F-actin-binding protein, neurabin-II/spinophilin. Ide N, et al. Biochem Biophys Res Commun, 1998 Mar 6. PMID 9514910
    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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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables PDZ domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables glutamate receptor binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to plasma membrane protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi to plasma membrane protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in phagophore assembly site ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in phagophore assembly site ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synaptic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    phagosome assembly factor 1
    Names
    UPF0183 protein C16orf70 homolog
    lin-10 homolog

    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_139040.2 → NP_620609.2  phagosome assembly factor 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/Swiss-Prot
      O08654
      UniProtKB/TrEMBL
      A6IYM3, G3V7W8
      Related
      ENSRNOP00000020003.2, ENSRNOT00000020003.4
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 407
      UPF0183; Uncharacterized protein family (UPF0183)

    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_086037.1 Reference GRCr8

      Range
      50011350..50050880
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039097464.2 → XP_038953392.1  phagosome assembly factor 1 isoform X2

      UniProtKB/Swiss-Prot
      O08654
      Related
      ENSRNOP00000111570.1, ENSRNOT00000137593.1
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 374
      UPF0183; Uncharacterized protein family (UPF0183)

    2. XM_039097463.2 → XP_038953391.1  phagosome assembly factor 1 isoform X1

      UniProtKB/Swiss-Prot
      O08654
      UniProtKB/TrEMBL
      A0A0G2JWC6
      Related
      ENSRNOP00000069827.1, ENSRNOT00000085891.3
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 395
      UPF0183; Uncharacterized protein family (UPF0183)

    3. XM_039097465.2 → XP_038953393.1  phagosome assembly factor 1 isoform X3

      UniProtKB/Swiss-Prot
      O08654
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 370
      UPF0183; Uncharacterized protein family (UPF0183)

    4. XM_063277774.1 → XP_063133844.1  phagosome assembly factor 1 isoform X5

    5. XM_063277773.1 → XP_063133843.1  phagosome assembly factor 1 isoform X4

      UniProtKB/Swiss-Prot
      O08654

    RNA

    1. XR_005496611.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O08654.1 GenPept UniProtKB/Swiss-Prot:O08654

    Gene LinkOut

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

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