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

Gene ID: 80262, updated on 25-Jan-2022

Summary

Official Symbol
PHAF1provided by HGNC
Official Full Name
phagosome 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; 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 2021]
Expression
Ubiquitous expression in skin (RPKM 9.9), liver (RPKM 9.8) and 25 other tissues See more
Orthologs
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Genomic context

See PHAF1 in Genome Data Viewer
Location:
16q22.1
Exon count:
19
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (67109881..67148544)
105.20201022 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 core-binding factor subunit beta 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

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
Component Evidence Code Pubs
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
phagosome assembly factor 1
Names
UPF0183 protein C16orf70

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_001320540.2NP_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
    UniProtKB/TrEMBL
    A0A024R6W4
    Conserved Domains (1) summary
    pfam03676
    Location:15407
    UPF0183; Uncharacterized protein family (UPF0183)
  2. NM_001320541.2NP_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
    UniProtKB/TrEMBL
    A0A024R6W4
    Conserved Domains (1) summary
    pfam03676
    Location:15407
    UPF0183; Uncharacterized protein family (UPF0183)
  3. NM_001320542.2NP_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
    UniProtKB/TrEMBL
    A0A024R6W4
    Related
    ENSP00000455182.1, ENST00000569600.5
    Conserved Domains (1) summary
    pfam03676
    Location:15407
    UPF0183; Uncharacterized protein family (UPF0183)
  4. NM_001320543.2NP_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:15379
    UPF0183; Uncharacterized protein family (UPF0183)
  5. NM_025187.5NP_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
    UniProtKB/TrEMBL
    A0A024R6W4
    Related
    ENSP00000219139.3, ENST00000219139.8
    Conserved Domains (1) summary
    pfam03676
    Location:15407
    UPF0183; Uncharacterized protein family (UPF0183)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    67109881..67148544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023730.1XP_016879219.1  phagosome assembly factor 1 isoform X3

    Conserved Domains (1) summary
    pfam03676
    Location:15309
    UPF0183; uncharacterized protein family (UPF0183)
  2. XM_017023731.1XP_016879220.1  phagosome assembly factor 1 isoform X4

  3. XM_017023729.1XP_016879218.1  phagosome assembly factor 1 isoform X1

    Conserved Domains (1) summary
    pfam03676
    Location:15504
    UPF0183; uncharacterized protein family (UPF0183)
  4. XM_006721284.3XP_006721347.1  phagosome assembly factor 1 isoform X1

    Conserved Domains (1) summary
    pfam03676
    Location:15504
    UPF0183; uncharacterized protein family (UPF0183)
  5. XM_011523350.3XP_011521652.1  phagosome assembly factor 1 isoform X2

    Conserved Domains (1) summary
    pfam03676
    Location:17499
    UPF0183; uncharacterized protein family (UPF0183)
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