U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

AGD5 ARF-GAP domain 5 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 835519, updated on 18-Sep-2024

Summary

Go to the top of the page Help
Official Symbol
AGD5
Official Full Name
ARF-GAP domain 5
Primary source
TAIR:AT5G54310
Locus tag
AT5G54310
See related
Araport:AT5G54310
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
ARF-GAP domain 5; AtAGD5; MDK4.13; MDK4_13; NEV; NEVERSHED
Summary
A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. Regulates membrane trafficking and organ separation.
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See AGD5 in Genome Data Viewer
Location:
chromosome: 5
Exon count:
11
Sequence:
Chromosome: 5; NC_003076.8 (22056986..22061270, complement)

Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene cytochrome c biogenesis protein family Neighboring gene cotton fiber-like protein (DUF761) Neighboring gene ncRNA Neighboring gene hypothetical protein (DUF295) Neighboring gene hypothetical protein (DUF295)

Genomic regions, transcripts, and products

Go to the top of the page Help
Genomic Sequence:
NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. Liljegren SJ, et al. Development, 2009 Jun. PMID 19429787, Free PMC Article
  2. NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana. Liu B, et al. J Exp Bot, 2013 Dec. PMID 23963677
  3. AGD5 is a GTPase-activating protein at the trans-Golgi network. Stefano G, et al. Plant J, 2010 Dec. PMID 21105926
  4. MTV1 and MTV4 encode plant-specific ENTH and ARF GAP proteins that mediate clathrin-dependent trafficking of vacuolar cargo from the trans-Golgi network. Sauer M, et al. Plant Cell, 2013 Jun. PMID 23771894, Free PMC Article
  5. Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves. Patharkar OR, et al. PLoS Genet, 2017 Dec. PMID 29253890, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. IDA and NEV function during both the cell-wall loosening and the cell separation stages of the abscission process. In addition, NEV acts to inhibit premature cell expansion.
    Title: NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana.
  2. Data indicate that MTV1 (AT3G16270) and AGD5 (AT5G54310) Physically Interact with clathrin.
    Title: MTV1 and MTV4 encode plant-specific ENTH and ARF GAP proteins that mediate clathrin-dependent trafficking of vacuolar cargo from the trans-Golgi network.
  3. AGD5, a a GTPase-activating protein, is distributed on a sub-population of the trans-Golgi network, where it co-localises with ARF1.
    Title: AGD5 is a GTPase-activating protein at the trans-Golgi network.
  4. NEV ARF-GAP activity at the trans-Golgi network and distinct endosomal compartments is required for the proper trafficking of cargo molecules required for cell separation. [NEV]
    Title: Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein.
Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help
NM_124811.5

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within defense response to Gram-negative bacterium IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within floral organ abscission IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in floral organ abscission IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within leaf abscission IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vesicle-mediated transport involved in floral organ abscission IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
ARF-GAP domain 5
NP_568807.1
  • ARF-GAP domain 5 (AGD5); FUNCTIONS IN: ARF GTPase activator activity, DNA binding, zinc ion binding; INVOLVED IN: floral organ abscission, activation of ARF GTPase activity; LOCATED IN: cytosol, trans-Golgi network, endosome, nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Arf GTPase activating protein (InterPro:IPR001164); BEST Arabidopsis thaliana protein match is: ARF-GAP domain 15 (TAIR:AT3G17660.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

Genome Annotation

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

Reference assembly

Genomic

  1. NC_003076.8 Reference assembly

    Range
    22056986..22061270 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_124811.5 → NP_568807.1  ARF-GAP domain 5 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_568807.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    C4NZX2, Q8L8M0, Q9FL69, Q9FVH4
    UniProtKB/TrEMBL
    A0A178UN58, A0A5S9YDY3, A0A654GB12
    Conserved Domains (2) summary
    COG5347
    Location:9 → 262
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
    cd08204
    Location:19 → 117
    ArfGap; GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9FL69.1

Gene LinkOut

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

Molecular Biology Databases
Research Materials
Tools