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    Phaf1 phagosome assembly factor 1 [ Mus musculus (house mouse) ]

    Gene ID: 234678, updated on 5-Mar-2024

    Summary

    Official Symbol
    Phaf1provided by MGI
    Official Full Name
    phagosome assembly factor 1provided by MGI
    Primary source
    MGI:MGI:2443049
    See related
    Ensembl:ENSMUSG00000031889 AllianceGenome:MGI:2443049
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Lin10; Mytho; D230025D16Rik
    Summary
    Predicted to enable PDZ domain binding activity and glutamate receptor binding activity. Predicted to be involved in Golgi to plasma membrane protein transport. Predicted to be located in membrane and phagophore assembly site. Predicted to be active in dendrite; synaptic vesicle membrane; and trans-Golgi network. Is expressed in several structures, including adrenal gland; genitourinary system; liver; lung; and spleen. Orthologous to human PHAF1 (phagosome assembly factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lung adult (RPKM 24.9), liver adult (RPKM 16.8) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Phaf1 in Genome Data Viewer
    Location:
    8 D3; 8 53.04 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (105951779..105979685)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (105225146..105253053)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 22063 Neighboring gene core binding factor beta Neighboring gene expressed sequence AI225912 Neighboring gene STARR-seq mESC enhancer starr_22523 Neighboring gene STARR-seq mESC enhancer starr_22525 Neighboring gene STARR-seq mESC enhancer starr_22526 Neighboring gene STARR-positive B cell enhancer mm9_chr8:107778026-107778327 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 Neighboring gene STARR-positive B cell enhancer ABC_E8260 Neighboring gene TNFRSF1A-associated via death domain Neighboring gene F-box and leucine-rich repeat protein 8

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    General gene information

    Markers

    Clone Names

    • MGC6480

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables glutamate receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    located_in phagophore assembly site ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synaptic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    phagosome assembly factor 1
    Names
    UPF0183 protein C16orf70 homolog
    lin-10 homolog

    NCBI Reference Sequences (RefSeq)

    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_001379098.1NP_001366027.1  phagosome assembly factor 1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC124713
      Conserved Domains (1) summary
      pfam03676
      Location:15437
      UPF0183; Uncharacterized protein family (UPF0183)
    2. NM_145604.3NP_663579.2  phagosome assembly factor 1 isoform 2

      See identical proteins and their annotated locations for NP_663579.2

      Status: VALIDATED

      Source sequence(s)
      AC124713
      Consensus CDS
      CCDS22593.1
      UniProtKB/Swiss-Prot
      Q6PER2, Q922R1
      Related
      ENSMUSP00000034361.4, ENSMUST00000034361.10
      Conserved Domains (1) summary
      pfam03676
      Location:15407
      UPF0183; Uncharacterized protein family (UPF0183)

    RNA

    1. NR_166491.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC124713
    2. NR_166492.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC124713
      Related
      ENSMUST00000141957.8
    3. NR_166493.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC124713
      Related
      ENSMUST00000124113.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000074.7 Reference GRCm39 C57BL/6J

      Range
      105951779..105979685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006530888.4XP_006530951.1  phagosome assembly factor 1 isoform X2

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:2256
      UPF0183; Uncharacterized protein family (UPF0183)
    2. XM_036153966.1XP_036009859.1  phagosome assembly factor 1 isoform X1

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:1267
      UPF0183; Uncharacterized protein family (UPF0183)
    3. XM_036153968.1XP_036009861.1  phagosome assembly factor 1 isoform X4

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:2226
      UPF0183; Uncharacterized protein family (UPF0183)
    4. XM_036153967.1XP_036009860.1  phagosome assembly factor 1 isoform X3

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:1237
      UPF0183; Uncharacterized protein family (UPF0183)