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    PHAF1 phagophore assembly factor 1 [ Homo sapiens (human) ]

    Gene ID: 80262, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PHAF1provided by HGNC
    Official Full Name
    phagophore assembly factor 1provided by HGNC
    Primary source
    HGNC:HGNC:29564
    See related
    Ensembl:ENSG00000125149 AllianceGenome:HGNC:29564
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LIN10; MYTHO; lin-10; C16orf6; C16orf70
    Summary
    Predicted to be involved in Golgi to plasma membrane protein transport. Located in phagophore assembly site. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in skin (RPKM 9.9), liver (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHAF1 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67109941..67148544)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72904233..72942836)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67143844..67182447)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 543, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7578 Neighboring gene core-binding factor subunit beta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67142676-67143418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67143419-67144160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67189519-67190420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7584 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67195788-67196300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67196374-67197322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67197323-67198271 Neighboring gene TNFRSF1A associated via death domain Neighboring gene F-box and leucine rich repeat protein 8 Neighboring gene heat shock transcription factor 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    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. Kinesin superfamily motor protein KIF17 and mLin-10 in NMDA receptor-containing vesicle transport. Setou M, et al. Science, 2000 Jun 9. PMID 10846156
    3. Mammalian BCAS3 and C16orf70 associate with the phagophore assembly site in response to selective and non-selective autophagy. Kojima W, et al. Autophagy, 2021 Aug. PMID 33499712, Free PMC Article
    4. Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response. Lou LQ, et al. J Mol Med (Berl), 2023 Mar. PMID 36629882
    5. Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph. Casabonne D, et al. Haematologica, 2011 Feb. PMID 21048031, Free PMC Article

    See all (29) 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.
    2. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12076

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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
    		  
    Component Evidence Code Pubs
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagophore assembly site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    phagosome assembly factor 1
    Names
    UPF0183 protein C16orf70
    macro-autophagy and youth optimizer

    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_001320540.2 → NP_001307469.1  phagosome assembly factor 1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AA127668, AL540304, BC004556, HY157930
      Consensus CDS
      CCDS10828.1
      UniProtKB/Swiss-Prot
      Q9BSU1, Q9HA86
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 407
      UPF0183; Uncharacterized protein family (UPF0183)

    2. NM_001320541.2 → NP_001307470.1  phagosome assembly factor 1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AA127668, BC004556, CB997191, HY157930
      Consensus CDS
      CCDS10828.1
      UniProtKB/Swiss-Prot
      Q9BSU1, Q9HA86
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 407
      UPF0183; Uncharacterized protein family (UPF0183)

    3. NM_001320542.2 → NP_001307471.1  phagosome assembly factor 1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AA127668, AF176088, BC004556, HY157930
      Consensus CDS
      CCDS10828.1
      UniProtKB/Swiss-Prot
      Q9BSU1, Q9HA86
      Related
      ENSP00000455182.1, ENST00000569600.5
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 407
      UPF0183; Uncharacterized protein family (UPF0183)

    4. NM_001320543.2 → NP_001307472.1  phagosome assembly factor 1 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AA127668, BC004556, CB997191, HY157930
      UniProtKB/Swiss-Prot
      Q9BSU1
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 379
      UPF0183; Uncharacterized protein family (UPF0183)

    5. NM_025187.5 → NP_079463.2  phagosome assembly factor 1 isoform a

      See identical proteins and their annotated locations for NP_079463.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AA127668, AC074143, BC004556, HY121038
      Consensus CDS
      CCDS10828.1
      UniProtKB/Swiss-Prot
      Q9BSU1, Q9HA86
      Related
      ENSP00000219139.3, ENST00000219139.8
      Conserved Domains (1) summary
      pfam03676
      Location:15 → 407
      UPF0183; Uncharacterized protein family (UPF0183)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      67109941..67148544
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721284.4 → XP_006721347.1  phagosome assembly factor 1 isoform X1

      Conserved Domains (1) summary
      pfam03676
      Location:15 → 504
      UPF0183; uncharacterized protein family (UPF0183)

    2. XM_017023729.2 → XP_016879218.1  phagosome assembly factor 1 isoform X1

      Conserved Domains (1) summary
      pfam03676
      Location:15 → 504
      UPF0183; uncharacterized protein family (UPF0183)

    3. XM_047434712.1 → XP_047290668.1  phagosome assembly factor 1 isoform X4

    4. XM_047434713.1 → XP_047290669.1  phagosome assembly factor 1 isoform X5

    5. XM_017023731.2 → XP_016879220.1  phagosome assembly factor 1 isoform X5

    6. XM_011523350.4 → XP_011521652.1  phagosome assembly factor 1 isoform X2

      Conserved Domains (1) summary
      pfam03676
      Location:17 → 499
      UPF0183; uncharacterized protein family (UPF0183)

    7. XM_047434711.1 → XP_047290667.1  phagosome assembly factor 1 isoform X3

    8. XM_047434714.1 → XP_047290670.1  phagosome assembly factor 1 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      72904233..72942836
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314038.1 → XP_054170013.1  phagosome assembly factor 1 isoform X1

    2. XM_054314039.1 → XP_054170014.1  phagosome assembly factor 1 isoform X1

    3. XM_054314042.1 → XP_054170017.1  phagosome assembly factor 1 isoform X4

    4. XM_054314044.1 → XP_054170019.1  phagosome assembly factor 1 isoform X5

    5. XM_054314043.1 → XP_054170018.1  phagosome assembly factor 1 isoform X5

    6. XM_054314045.1 → XP_054170020.1  phagosome assembly factor 1 isoform X6

    7. XM_054314040.1 → XP_054170015.1  phagosome assembly factor 1 isoform X2

    8. XM_054314041.1 → XP_054170016.1  phagosome assembly factor 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BSU1.1 GenPept UniProtKB/Swiss-Prot:Q9BSU1

    Gene LinkOut

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

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