RCF3 RNA-binding KH domain-containing protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: RCF3
Official Full Name: RNA-binding KH domain-containing protein
Primary source: TAIR:AT5G53060
Locus tag: AT5G53060
See related: Araport:AT5G53060
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: MNB8.12; MNB8_12; regulator of CBF gene expression 3; SHI1; SHINY 1
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Genomic context

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See RCF3 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 9

Sequence:: Chromosome: 5; NC_003076.8 (21514896..21520421)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1.
Title: KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1.
HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5)affects the biogenesis of a subset of miRNA.
Title: The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.
a KH domain-containing putative RNA-binding protein RCF3 is an important upstream regulator for heat stress-responsive gene expression and thermotolerance in Arabidopsis [RCF3]
Title: A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis.
In fry2 mutants, HOS5 failed to be localized in nuclear speckles but was found mainly in the nucleoplasm. hos5 mutants were impaired in mRNA export and accumulated a significant amount of mRNA in the nuclei, particularly under salt stress conditions. [HOS5]
Title: A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.
K-homology domain-containing protein named SHINY1 (SHI1) interacts with CPL1 to modulate gene expression. [SHI1] [SHINY1]
Title: The arabidopsis RNA binding protein with K homology motifs, SHINY1, interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress stress-inducible gene expression.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001203597.1

Supported by ESTs:

NM_001345032.1

Supported by ESTs:

NM_124685.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables primary miRNA 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 heat acclimation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within jasmonic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within primary miRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of defense response to fungus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to osmotic stress	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nuclear dicing body	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: RNA-binding KH domain-containing protein

NP_001190526.1

RNA-binding KH domain-containing protein; FUNCTIONS IN: RNA binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: K Homology, type 1, subgroup (InterPro:IPR018111), K Homology (InterPro:IPR004087), K Homology, type 1 (InterPro:IPR004088); BEST Arabidopsis thaliana protein match is: RNA-binding KH domain-containing protein (TAIR:AT5G15270.1).

NP_200118.3

RNA-binding KH domain-containing protein; FUNCTIONS IN: RNA binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: K Homology, type 1, subgroup (InterPro:IPR018111), K Homology (InterPro:IPR004087), K Homology, type 1 (InterPro:IPR004088); BEST Arabidopsis thaliana protein match is: RNA-binding KH domain-containing protein (TAIR:AT5G15270.1); Has 2883 Blast hits to 1912 proteins in 183 species: Archae - 0; Bacteria - 2; Metazoa - 1739; Fungi - 239; Plants - 817; Viruses - 2; Other Eukaryotes - 84 (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

NC_003076.8 Reference assembly

Range

21514896..21520421

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_124685.4 → NP_200118.3 RNA-binding KH domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_200118.3

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8W4B1, Q9LVU6

UniProtKB/TrEMBL

A0A178UIE3, A0A5S9YDN8, A0A654GAE7

Conserved Domains (3) summary

cd22459
Location:67 → 140

KH-I_PEPPER_rpt1_like; first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins

cd22460
Location:178 → 250

KH-I_PEPPER_rpt2_like; second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins

cd22463
Location:576 → 644

KH-I_RCF3_like_rpt5; fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein
NM_001345032.1 → NP_001330551.1 RNA-binding KH domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8BB62, A0A5S9YDN8, A0A654GAE7
NM_001203597.1 → NP_001190526.1 RNA-binding KH domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001190526.1

Status: REVIEWED

UniProtKB/TrEMBL

F4KIZ8

Conserved Domains (1) summary

cd02396
Location:69 → 143

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...