LXL04_002239 | RubberDandelionOmics

Gene overview

LXL04_002239

Reference: OH-1004 Chr: Chr01 Coordinates: 44470335-44473579 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2280 bp · LXL04_002239|LXL04_002239|OH1004|cDNA

ATGTCAAATAGCATTGTTACGAACATACAATTGACCATAGAGGAAGGGAGACAAGCGTTTTCTGAATTCCAGAACATGATAGAGTGTTTAGaggaaaagaaacacgacaaCACCCCTCTACAATATTTCGGTTATTCAGtTAAGTTAGTGCTGGGAGGGTCAGTTAAGACCGCGATGGCGCCCCCAGCCGTCACCACCACTTTGGTCACTCCGAAGAGCAACCCACCGATCCTTAGGAACCCCCGGACAACTAGGGTAAA...

CDS

Download CDS FASTA

2280 bp · LXL04_002239|LXL04_002239|OH1004|CDS

ATGTCAAATAGCATTGTTACGAACATACAATTGACCATAGAGGAAGGGAGACAAGCGTTTTCTGAATTCCAGAACATGATAGAGTGTTTAGAGGAAAAGAAACACGACAACACCCCTCTACAATATTTCGGTTATTCAGTTAAGTTAGTGCTGGGAGGGTCAGTTAAGACCGCGATGGCGCCCCCAGCCGTCACCACCACTTTGGTCACTCCGAAGAGCAACCCACCGATCCTTAGGAACCCCCGGACAACTAGGGTAAA...

Protein

Download Protein FASTA

759 aa · LXL04_002239|LXL04_002239|OH1004|PROTEIN

MSNSIVTNIQLTIEEGRQAFSEFQNMIECLEEKKHDNTPLQYFGYSVKLVLGGSVKTAMAPPAVTTTLVTPKSNPPILRNPRTTRVNPDASPQDSNLRPPLGKPRTIAKRPGVTCMSMDGSFPNKRLFDHSTSDRSDHPHLTPTSSNKRRHQHHHPHPSSPATPQSNNNNPFRASLKLSSGETLFRILCPSAKTGGVIGKGGAIIRQFREETGAKIRIDDYTHGSEERVIVIVAECTHKNKDIPNNNNDDSNSEESGNSN...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_002239`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_002239

Location Chr01:44470335-44473579 (-)

Description Similar to RCF3: RNA-binding KH domain-containing protein RCF3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g53060`	Acts as a negative regulator of osmotic stress-induced gene expression.	HOS5-a negative regulator of osmotic stress-induced gene expression in Arabidopsis thaliana.1999 · DOI: 10.1046/j.1365-313x.1999.00558.x A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis.2013 · DOI: 10.1093/mp/sss119 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.2013 · DOI: 10.1371/journal.pgen.1003625 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.2013 · DOI: 10.1371/journal.pgen.1003875 The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress.2015 · DOI: 10.1371/journal.pone.0126978 The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.2015 · DOI: 10.1093/nar/gkv751 KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1.2015 · DOI: 10.1073/pnas.1512865112
`At4g18375`	KH domain-containing protein At4g18375.	No verified direct reference in this release
`At5g64390`	Functions in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA.	No verified direct reference in this release
`At3g04610`	Positively regulates flowering by repressing FLC expression and post-transcriptional modification.	No verified direct reference in this release
`At4g26000`	Regulates vegetative and gynoecium development.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002239 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006396 RNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0010093 specification of floral organ identity Biological Process

GO:0010286 heat acclimation Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0030154 cell differentiation Biological Process

GO:0031053 primary miRNA processing Biological Process

GO:0048497 maintenance of floral organ identity Biological Process

KEGG gene cross-reference

ath:AT4G18375

ath:AT5G53060

ath:AT5G64390

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

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Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.800

Rank 1 · LXL04_002239 · OH-1004

Cytoplasm0.296

Rank 2 · LXL04_002239 · OH-1004

Cell membrane0.043

Rank 3 · LXL04_002239 · OH-1004

Endoplasmic reticulum0.025

Rank 4 · LXL04_002239 · OH-1004

Lysosome / Vacuole0.015

Rank 5 · LXL04_002239 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00013.36KH_1185-233 aa

PF00013.36KH_1313-379 aa

PF00013.36KH_1426-475 aa

PF00013.36KH_1518-584 aa

PF00013.36KH_1689-747 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002239	`PF00013.36`	KH_1	185	233	1.1e-64	214.7
LXL04_002239	`PF00013.36`	KH_1	313	379	1.1e-64	214.7
LXL04_002239	`PF00013.36`	KH_1	426	475	1.1e-64	214.7
LXL04_002239	`PF00013.36`	KH_1	518	584	1.1e-64	214.7
LXL04_002239	`PF00013.36`	KH_1	689	747	1.1e-64	214.7

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8W4B1`	Arabidopsis thaliana	RNA-binding KH domain-containing protein RCF3	31.760%	Swiss-Prot	moderate database homology
`P58223`	Arabidopsis thaliana	KH domain-containing protein At4g18375	27.935%	Swiss-Prot	weak database homology
`F4KDN0`	Arabidopsis thaliana	KH domain-containing protein HEN4	32.020%	Swiss-Prot	weak database homology
`Q9SR13`	Arabidopsis thaliana	Flowering locus K homology domain	28.571%	Swiss-Prot	weak database homology
`Q9SZH4`	Arabidopsis thaliana	RNA-binding KH domain-containing protein PEPPER	25.978%	Swiss-Prot	weak database homology

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