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

Gene ID: 234678, updated on 5-Mar-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 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
human all
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Genomic context

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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. 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
  2. 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
  3. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article
  4. 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
  5. Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, et al. PLoS Biol, 2003 Dec. PMID 14691545, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

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
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

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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

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