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FDM1 XH/XS domain-containing protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 838161, updated on 18-Sep-2024

Summary

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Official Symbol
FDM1
Official Full Name
XH/XS domain-containing protein
Primary source
TAIR:AT1G15910
Locus tag
AT1G15910
See related
Araport:AT1G15910
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
factor of DNA methylation 1; IDN2 PARALOG 1; IDNL1; IDP1; INVOLVED IN DE NOVO 2 (IDN2) - LIKE 1; T24D18.1; T24D18_1
Summary
Belongs to a subgroup of SGS3-like proteins that act redundantly in RNA-directed DNA methylation: AT1G15910 (FDM1), AT4G00380 (FDM2), AT3G12550 (FDM3), AT1G13790 (FDM4), AT1G80790 (FDM5).
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Genomic context

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See FDM1 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
7
Sequence:
Chromosome: 1; NC_003070.9 (5465251..5469180)

Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Disease resistance protein (CC-NBS-LRR class) family Neighboring gene uncharacterized protein Neighboring gene Polynucleotidyl transferase, ribonuclease H-like superfamily protein Neighboring gene Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Expression analysis of Arabidopsis XH/XS-domain proteins indicates overlapping and distinct functions for members of this gene family. Butt H, et al. J Exp Bot, 2014 Mar. PMID 24574485, Free PMC Article
  2. The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation. Xie M, et al. Plant J, 2012 Nov. PMID 22757778
  3. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Ausin I, et al. Proc Natl Acad Sci U S A, 2012 May 29. PMID 22592791, Free PMC Article
  4. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. Zhang CJ, et al. PLoS Genet, 2012. PMID 22570638, Free PMC Article
  5. IDN2 Interacts with RPA and Facilitates DNA Double-Strand Break Repair by Homologous Recombination in Arabidopsis. Liu M, et al. Plant Cell, 2017 Mar. PMID 28223440, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Fluorescent protein-tagged FDM genes were expressed either in nuclei or in the cytoplasm, suggestive of activities of XH/XS-domain proteins in association with chromatin as well as outside the nuclear compartment.
    Title: Expression analysis of Arabidopsis XH/XS-domain proteins indicates overlapping and distinct functions for members of this gene family.
  2. XH domain-mediated complex formation of FDM1 is required for its function in RNA-directed DNA methylation pathway (RdDM).
    Title: The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation.
  3. Data show that two partially redundant proteins termed IDN2-LIKE 1 (IDNL1; AT1G15910) and IDN2-LIKE 2 (IDNL2; AT4G00380) that are paralogous to INVOLVED IN DE NOVO 2 (IDN2) and that form a stable complex with IDN2 in vivo.
    Title: INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_101459.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded RNA binding 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 gene silencing by siRNA-directed DNA methylation IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm ISM
Inferred from Sequence Model
more info
  
located_in plasmodesma HDA PubMed 

General protein information

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Preferred Names
XH/XS domain-containing protein
NP_173043.1
  • XH/XS domain-containing protein; CONTAINS InterPro DOMAIN/s: Domain of unknown function XS (InterPro:IPR005380), Domain of unknown function XH (InterPro:IPR005379), Domain of unknown function, putative Zinc finger, XS/XH (InterPro:IPR005381); BEST Arabidopsis thaliana protein match is: XH/XS domain-containing protein (TAIR:AT4G00380.1); Has 48628 Blast hits to 29972 proteins in 1836 species: Archae - 567; Bacteria - 5701; Metazoa - 24120; Fungi - 3416; Plants - 1878; Viruses - 163; Other Eukaryotes - 12783 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

  1. NC_003070.9 Reference assembly

    Range
    5465251..5469180
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_101459.4 → NP_173043.1  XH/XS domain-containing protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_173043.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9S9P3
    UniProtKB/TrEMBL
    A0A178W3T4, A0A5S9ULZ1
    Conserved Domains (4) summary
    COG1196
    Location:211 → 485
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam03470
    Location:41 → 83
    zf-XS; XS zinc finger domain
    pfam03468
    Location:117 → 224
    XS; XS domain
    pfam03469
    Location:502 → 632
    XH; XH domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9S9P3.1

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