LXL04_036404 | RubberDandelionOmics

Gene overview

LXL04_036404

Reference: OH-1004 Chr: Chr08 Coordinates: 41378259-41387038 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1149 bp · LXL04_036404|LXL04_036404|OH1004|cDNA

ATGGGAGAGGAAGTGAGAATCAACGAGTTTAACGATGTCGGCGGGGAGGATGATGATCGAGTTTTGGAGTGGGAGGCCGGTTTGCCTAGCGTTGATGATTTAATGCCGTTGTCACAGTCGCTGGTACCGGCGGAACTGGCATCGGCGTTCAGCATCACGCCGGAGCCTCACCGGAGTATGATTGACGTCAATCGCGCTTCTCAAAACACACTATCGAATCTCCGAGGGCAGTCGGTGAAACCGACGCTGAATAAATTTCA...

CDS

Download CDS FASTA

1149 bp · LXL04_036404|LXL04_036404|OH1004|CDS

ATGGGAGAGGAAGTGAGAATCAACGAGTTTAACGATGTCGGCGGGGAGGATGATGATCGAGTTTTGGAGTGGGAGGCCGGTTTGCCTAGCGTTGATGATTTAATGCCGTTGTCACAGTCGCTGGTACCGGCGGAACTGGCATCGGCGTTCAGCATCACGCCGGAGCCTCACCGGAGTATGATTGACGTCAATCGCGCTTCTCAAAACACACTATCGAATCTCCGAGGGCAGTCGGTGAAACCGACGCTGAATAAATTTCA...

Protein

Download Protein FASTA

382 aa · LXL04_036404|LXL04_036404|OH1004|PROTEIN

MGEEVRINEFNDVGGEDDDRVLEWEAGLPSVDDLMPLSQSLVPAELASAFSITPEPHRSMIDVNRASQNTLSNLRGQSVKPTLNKFHGFKSFGDEKGDEMVMEGEETADLTGDCSDSRKLRRVDSGGTGAIGGAGEEADSALRADDSSARTSKRPRLVWTPQLHKRFVDVVAHLGVKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQGLSNEGPSSSDHLFASTPVPQSLHESSGGGNGNGNSHAPPLPIPMPY...

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_036404`
TK1151 ID	TkA04G049660
OH-1004 ID	LXL04_036404
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.400
Protein coverage (%)	TK1151 98.154 / OH-1004 83.770 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_036404

Location Chr08:41378259-41387038 (+)

Description Similar to LUX: Transcription factor LUX

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g46640`	Transcription factor that is essential for the generation of the circadian clock oscillation.	PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock.2005 · DOI: 10.1111/j.1365-2443.2005.00892.x LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.2011 · DOI: 10.1016/j.cub.2010.12.021
`At5g59570`	Transcription factor that is a critical component of the regulatory circuit of the circadian clock.	No verified direct reference in this release
`At2g40970`	Probable transcription factor that acts as a negative regulator of freezing tolerance via a CBF-independent pathway.	A single-repeat R3-MYB transcription factor MYBC1 negatively regulates freezing tolerance in Arabidopsis.2010 · DOI: 10.1016/j.bbrc.2010.03.114

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2XE31`	Transcriptional activator that binds specific DNA sequence.	No verified direct reference in this release
`Os03g0224200`	Transcriptional activator that binds specific DNA sequence.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_036404 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0000160 phosphorelay signal transduction system Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009409 response to cold Biological Process

GO:0009736 cytokinin-activated signaling pathway Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0042752 regulation of circadian rhythm Biological Process

GO:0042753 positive regulation of circadian rhythm Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G40970

ath:AT3G46640

ath:AT5G59570

dosa:Os03g0224200

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.

Nucleus0.972

Rank 1 · LXL04_036404 · OH-1004

Cytoplasm0.093

Rank 2 · LXL04_036404 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_036404 · OH-1004

Endoplasmic reticulum0.015

Rank 4 · LXL04_036404 · OH-1004

Plastid0.010

Rank 5 · LXL04_036404 · 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.

PF00249.38Myb_DNA-binding157-206 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036404	`PF00249.38`	Myb_DNA-binding	157	206	1.9e-08	35.0

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
`Q9SNB4`	Arabidopsis thaliana	Transcription factor LUX	50.146%	Swiss-Prot	strong database homology
`Q9LTH4`	Arabidopsis thaliana	Transcription factor BOA	54.941%	Swiss-Prot	moderate database homology
`O22210`	Arabidopsis thaliana	Transcription factor MYBC1	44.595%	Swiss-Prot	moderate database homology
`A2XE31`	Oryza sativa subsp. indica	Two-component response regulator ORR21	67.188%	Swiss-Prot	weak database homology
`Q8H7S7`	Oryza sativa subsp. japonica	Two-component response regulator ORR21	67.188%	Swiss-Prot	weak database homology

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