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FDM5 XH/XS domain-containing protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 844418, updated on 18-Sep-2024

Summary

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Official Symbol
FDM5
Official Full Name
XH/XS domain-containing protein
Primary source
TAIR:AT1G80790
Locus tag
AT1G80790
See related
Araport:AT1G80790
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
F23A5.14; F23A5_14; factor of DNA methylation 5
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 FDM5 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
9
Sequence:
Chromosome: 1; NC_003070.9 (30359649..30363427)

Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene P-loop containing nucleoside triphosphate hydrolases superfamily protein Neighboring gene Polynucleotidyl transferase, ribonuclease H-like superfamily protein Neighboring gene miscRNA Neighboring gene Tudor/PWWP/MBT 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_001335010.1
NM_106727.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in gene silencing by siRNA-directed DNA methylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus ISM
Inferred from Sequence Model
more info
  

General protein information

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Preferred Names
XH/XS domain-containing protein
NP_178194.1
  • 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:AT1G15910.1); Has 81745 Blast hits to 47168 proteins in 2099 species: Archae - 1218; Bacteria - 10615; Metazoa - 37220; Fungi - 5411; Plants - 3180; Viruses - 320; Other Eukaryotes - 23781 (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
    30359649..30363427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001335009.1 → NP_001321040.1  XH/XS domain-containing protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    B9DHL1, Q0WUU8, Q9SAI1
    UniProtKB/TrEMBL
    A0A178WF73, A0A5S9WW61, A0A654EVW5
    Conserved Domains (4) summary
    pfam03470
    Location:42 → 84
    zf-XS; XS zinc finger domain
    TIGR02169
    Location:238 → 429
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    pfam03469
    Location:501 → 632
    XH; XH domain
    cd12266
    Location:118 → 222
    RRM_like_XS; RNA recognition motif (RRM)-like XS domain found in plants

  2. NM_106727.4 → NP_178194.1  XH/XS domain-containing protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_178194.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    B9DHL1, Q0WUU8, Q9SAI1
    UniProtKB/TrEMBL
    A0A178WF73, A0A5S9WW61, A0A654EVW5
    Conserved Domains (4) summary
    pfam03470
    Location:42 → 84
    zf-XS; XS zinc finger domain
    TIGR02169
    Location:238 → 429
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    pfam03469
    Location:501 → 632
    XH; XH domain
    cd12266
    Location:118 → 222
    RRM_like_XS; RNA recognition motif (RRM)-like XS domain found in plants

  3. NM_001335010.1 → NP_001321039.1  XH/XS domain-containing protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1P8APP5
    Conserved Domains (3) summary
    pfam03470
    Location:42 → 84
    zf-XS; XS zinc finger domain
    TIGR02169
    Location:238 → 429
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    cd12266
    Location:118 → 222
    RRM_like_XS; RNA recognition motif (RRM)-like XS domain found in plants
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9SAI1.1

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