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Phaf1 phagophore assembly factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 207123, updated on 27-Nov-2024

Summary

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Official Symbol
Phaf1provided by RGD
Official Full Name
phagophore assembly factor 1provided by RGD
Primary source
RGD:621098
See related
EnsemblRapid:ENSRNOG00000014668 AllianceGenome:RGD:621098
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Lin10; Lin-10; RGD621098
Summary
Enables PDZ domain binding activity and glutamate receptor binding activity. Involved in Golgi to plasma membrane protein transport. Located in dendrite; synaptic vesicle membrane; and trans-Golgi network. Orthologous to human PHAF1 (phagosome assembly factor 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Adrenal (RPKM 149.8), Lung (RPKM 146.3) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Phaf1 in Genome Data Viewer
Location:
19q11
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (50011350..50050880)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (33101453..33138920)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (37179850..37207714)

Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene core-binding factor subunit beta Neighboring gene ribosomal protein L27, pseudogene 10 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 Neighboring gene microtubule associated tyrosine carboxypeptidase 1 Neighboring gene nucleolar protein 3 Neighboring gene exocyst complex component 3-like 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. The PDZ domains of mLin-10 regulate its trans-Golgi network targeting and the surface expression of AMPA receptors. Stricker NL, et al. Neuropharmacology, 2003 Nov. PMID 14529721
  2. Molecular cloning and characterization of rat lin-10. Ide N, et al. Biochem Biophys Res Commun, 1998 Feb 13. PMID 9480860
  3. Interaction of rat lin-10 with brain-enriched F-actin-binding protein, neurabin-II/spinophilin. Ide N, et al. Biochem Biophys Res Commun, 1998 Mar 6. PMID 9514910
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables PDZ domain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables glutamate receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
involved_in Golgi to plasma membrane protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 

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_139040.2 → NP_620609.2  phagosome assembly factor 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000019
    UniProtKB/Swiss-Prot
    O08654
    UniProtKB/TrEMBL
    A6IYM3, G3V7W8
    Related
    ENSRNOP00000020003.2, ENSRNOT00000020003.4
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 407
    UPF0183; Uncharacterized protein family (UPF0183)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086037.1 Reference GRCr8

    Range
    50011350..50050880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039097464.2 → XP_038953392.1  phagosome assembly factor 1 isoform X2

    UniProtKB/Swiss-Prot
    O08654
    Related
    ENSRNOP00000111570.1, ENSRNOT00000137593.1
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 374
    UPF0183; Uncharacterized protein family (UPF0183)

  2. XM_039097463.2 → XP_038953391.1  phagosome assembly factor 1 isoform X1

    UniProtKB/Swiss-Prot
    O08654
    UniProtKB/TrEMBL
    A0A0G2JWC6
    Related
    ENSRNOP00000069827.1, ENSRNOT00000085891.3
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 395
    UPF0183; Uncharacterized protein family (UPF0183)

  3. XM_039097465.2 → XP_038953393.1  phagosome assembly factor 1 isoform X3

    UniProtKB/Swiss-Prot
    O08654
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 370
    UPF0183; Uncharacterized protein family (UPF0183)

  4. XM_063277774.1 → XP_063133844.1  phagosome assembly factor 1 isoform X5

  5. XM_063277773.1 → XP_063133843.1  phagosome assembly factor 1 isoform X4

RNA

  1. XR_005496611.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O08654.1 GenPept UniProtKB/Swiss-Prot:O08654

Gene LinkOut

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