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FDM4 XH/XS domain-containing protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 837939, updated on 18-Sep-2024

Summary

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Official Symbol
FDM4
Official Full Name
XH/XS domain-containing protein
Primary source
TAIR:AT1G13790
Locus tag
AT1G13790
See related
Araport:AT1G13790
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
F16A14.2; F16A14_2; factor of DNA methylation 4
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 FDM4 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
7
Sequence:
Chromosome: 1; NC_003070.9 (4726770..4730425)

Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene root UVB sensitive protein (Protein of unknown function, DUF647) Neighboring gene F-box/RNI-like/FBD-like domains-containing protein Neighboring gene uncharacterized protein Neighboring gene Tetratricopeptide repeat (TPR)-like superfamily protein Neighboring gene Restriction endonuclease, type II-like superfamily 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. A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation. Xie M, et al. Nucleic Acids Res, 2012 May. PMID 22302148, Free PMC Article
  2. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

GeneRIFs: Gene References Into Functions

General gene information

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Homology

NM_001332088.1
NM_101247.3

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  

General protein information

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Preferred Names
XH/XS domain-containing protein
NP_001318996.1
  • 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:AT3G48670.2); Has 49019 Blast hits to 30980 proteins in 1872 species: Archae - 565; Bacteria - 6337; Metazoa - 23607; Fungi - 3326; Plants - 1659; Viruses - 198; Other Eukaryotes - 13327 (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
    4726770..4730425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001332088.1 → NP_001318996.1  XH/XS domain-containing protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9LMH6
    UniProtKB/TrEMBL
    A0A178W5G1, A0A5S9U8W3
    Conserved Domains (4) summary
    COG5281
    Location:301 → 543
    COG5281; Phage-related minor tail protein [Mobilome: prophages, transposons]
    pfam03470
    Location:34 → 76
    zf-XS; XS zinc finger domain
    pfam03468
    Location:216 → 330
    XS; XS domain
    pfam03469
    Location:602 → 726
    XH; XH domain

  2. NM_101247.3 → NP_172834.1  XH/XS domain-containing protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_172834.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9LMH6
    UniProtKB/TrEMBL
    A0A178W5G1, A0A5S9U8W3
    Conserved Domains (4) summary
    COG5281
    Location:301 → 543
    COG5281; Phage-related minor tail protein [Mobilome: prophages, transposons]
    pfam03470
    Location:34 → 76
    zf-XS; XS zinc finger domain
    pfam03468
    Location:216 → 330
    XS; XS domain
    pfam03469
    Location:602 → 726
    XH; XH domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9LMH6.1

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