LXL04_006309 | RubberDandelionOmics

Gene overview

LXL04_006309

Reference: OH-1004 Chr: Chr02 Coordinates: 6597312-6599813 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1614 bp · LXL04_006309|LXL04_006309|OH1004|cDNA

ATGGCTGGGCAAAGAAGTAGCAGTCATGGAAAACGTTCACACTCTCAATCCGACTACAGTGACCATGGAAGAAGCAGCAAAAGACGTAACAACAGTGATGACAGAGGCCAAAACTCAATCGGATCAGATGACACAGTGTACCGCTACTTATGCCCTAGTAAGCGAATCGGAAGCATAATGGGACGTGGTGGTGATATAATCAAGCAACTGAGATCTGAAAGCAAGTCCAAAATCAGAATTGGGGAGACTGTTTCAGGGTG...

CDS

Download CDS FASTA

1614 bp · LXL04_006309|LXL04_006309|OH1004|CDS

ATGGCTGGGCAAAGAAGTAGCAGTCATGGAAAACGTTCACACTCTCAATCCGACTACAGTGACCATGGAAGAAGCAGCAAAAGACGTAACAACAGTGATGACAGAGGCCAAAACTCAATCGGATCAGATGACACAGTGTACCGCTACTTATGCCCTAGTAAGCGAATCGGAAGCATAATGGGACGTGGTGGTGATATAATCAAGCAACTGAGATCTGAAAGCAAGTCCAAAATCAGAATTGGGGAGACTGTTTCAGGGTG...

Protein

Download Protein FASTA

537 aa · LXL04_006309|LXL04_006309|OH1004|PROTEIN

MAGQRSSSHGKRSHSQSDYSDHGRSSKRRNNSDDRGQNSIGSDDTVYRYLCPSKRIGSIMGRGGDIIKQLRSESKSKIRIGETVSGCDERVVTIHSTSDETNDFDDNDDRVCPAMDALFKVYDRVVADDLADDQDPEETPQVTVRLLVPSDQIGCVIGKGGQIVQNIRTDTGAQVRIVKDNHLPACALSSDELVQISGEASVVRKALFQISTRLHDNPSRSQHLLSSSSTPNLYPSGGGGGGSLMGAPGGPPIMGLTPLV...

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_006309`
TK1151 ID	TkA03G607590
OH-1004 ID	LXL04_006309
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	71.900
Protein coverage (%)	TK1151 80.423 / OH-1004 36.499 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_006309

Location Chr02:6597312-6599813 (+)

Description Similar to At4g18375: KH domain-containing protein At4g18375

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g18375`	KH domain-containing protein At4g18375.	No verified direct reference in this release
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006309 · 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:0010286 heat acclimation Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0031053 primary miRNA processing Biological Process

GO:1900150 regulation of defense response to fungus Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0010445 nuclear dicing body Cellular Component

KEGG gene cross-reference

ath:AT4G18375

ath:AT5G53060

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.

View expression for this gene

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.

Nucleus0.914

Rank 1 · LXL04_006309 · OH-1004

Cytoplasm0.202

Rank 2 · LXL04_006309 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_006309 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_006309 · OH-1004

Lysosome / Vacuole0.013

Rank 5 · LXL04_006309 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF00013.36KH_147-99 aa

PF00013.36KH_1143-210 aa

PF00013.36KH_1292-341 aa

PF00013.36KH_1377-441 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006309	`PF00013.36`	KH_1	47	99	2.3e-55	184.9
LXL04_006309	`PF00013.36`	KH_1	143	210	2.3e-55	184.9
LXL04_006309	`PF00013.36`	KH_1	292	341	2.3e-55	184.9
LXL04_006309	`PF00013.36`	KH_1	377	441	2.3e-55	184.9

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`P58223`	Arabidopsis thaliana	KH domain-containing protein At4g18375	31.772%	Swiss-Prot	moderate database homology
`Q8W4B1`	Arabidopsis thaliana	RNA-binding KH domain-containing protein RCF3	31.555%	Swiss-Prot	moderate database homology
`F4KDN0`	Arabidopsis thaliana	KH domain-containing protein HEN4	35.000%	Swiss-Prot	weak database homology
`Q9SR13`	Arabidopsis thaliana	Flowering locus K homology domain	34.682%	Swiss-Prot	weak database homology

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