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

    Gene ID: 234678, updated on 27-Nov-2024

    Summary

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    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 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, Nov 2024]
    Expression
    Ubiquitous expression in lung adult (RPKM 24.9), liver adult (RPKM 16.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    Related articles in PubMed

    1. C16ORF70/MYTHO promotes healthy aging in C.elegans and prevents cellular senescence in mammals. Franco-Romero A, et al. J Clin Invest, 2024 Jun 13. PMID 38869949, Free PMC Article
    2. MYTHO is a novel regulator of skeletal muscle autophagy and integrity. Leduc-Gaudet JP, et al. Nat Commun, 2023 Mar 2. PMID 36864049, Free PMC Article
    3. Urogenital and caudal dysgenesis in adrenocortical dysplasia (acd) mice is caused by a splicing mutation in a novel telomeric regulator. Keegan CE, et al. Hum Mol Genet, 2005 Jan 1. PMID 15537664
    4. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article
    5. Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Evsikov AV, et al. Genes Dev, 2006 Oct 1. PMID 17015433, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. C16ORF70/MYTHO promotes healthy aging in C.elegans and prevents cellular senescence in mammals.
      Title: C16ORF70/MYTHO promotes healthy aging in C.elegans and prevents cellular senescence in mammals.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    General gene information

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    Markers

    Homology

    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
    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
    		  
    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 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

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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_001379098.1 → NP_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:15 → 437
      UPF0183; Uncharacterized protein family (UPF0183)

    2. NM_145604.3 → NP_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:15 → 407
      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_006530888.4 → XP_006530951.1  phagosome assembly factor 1 isoform X2

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:2 → 256
      UPF0183; Uncharacterized protein family (UPF0183)

    2. XM_036153966.1 → XP_036009859.1  phagosome assembly factor 1 isoform X1

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:1 → 267
      UPF0183; Uncharacterized protein family (UPF0183)

    3. XM_036153968.1 → XP_036009861.1  phagosome assembly factor 1 isoform X4

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:2 → 226
      UPF0183; Uncharacterized protein family (UPF0183)

    4. XM_036153967.1 → XP_036009860.1  phagosome assembly factor 1 isoform X3

      UniProtKB/TrEMBL
      Q3TKL5
      Conserved Domains (1) summary
      pfam03676
      Location:1 → 237
      UPF0183; Uncharacterized protein family (UPF0183)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q922R1.2 GenPept UniProtKB/Swiss-Prot:Q922R1

    Gene LinkOut

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

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