LXL04_017843 | RubberDandelionOmics

Gene overview

LXL04_017843

Reference: OH-1004 Chr: Chr04 Coordinates: 2259071-2260390 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

987 bp · LXL04_017843|LXL04_017843|OH1004|cDNA

ATGGGAGAGGAAGTCAGAATTAGCGACTACGATGTCAGCGGTGGAGATGACGACGACCGAGTATCAGAGTGGGAAGCTGGGTTGCCGAACGTTGACGACTTACCGTCGTTGTCACAGTTGCTTATATCGGCAGAGATGGCGTCAGCTTTCAGCATCACAGCCGCCCCTCACCGGAGTATGGTTGACGTTGACCGCGCTTCTCGTGACACAGTTTCAAGTCTCCAAGGGCAGTCGCAACAACATCAGGTGAATAAACTTAC...

CDS

Download CDS FASTA

987 bp · LXL04_017843|LXL04_017843|OH1004|CDS

ATGGGAGAGGAAGTCAGAATTAGCGACTACGATGTCAGCGGTGGAGATGACGACGACCGAGTATCAGAGTGGGAAGCTGGGTTGCCGAACGTTGACGACTTACCGTCGTTGTCACAGTTGCTTATATCGGCAGAGATGGCGTCAGCTTTCAGCATCACAGCCGCCCCTCACCGGAGTATGGTTGACGTTGACCGCGCTTCTCGTGACACAGTTTCAAGTCTCCAAGGGCAGTCGCAACAACATCAGGTGAATAAACTTAC...

Protein

Download Protein FASTA

328 aa · LXL04_017843|LXL04_017843|OH1004|PROTEIN

MGEEVRISDYDVSGGDDDDRVSEWEAGLPNVDDLPSLSQLLISAEMASAFSITAAPHRSMVDVDRASRDTVSSLQGQSQQHQVNKLTDSKSFSDDRDEEMVVEGEETFDLTPDGSDSRKLRRVDSGGASGGAVEDAHSAMRADDTSTKTLKRIRLVWTPQLHKRFVEVVAHLGLKKAVPKTIMQMMNVEGLSRENVASHLQKYRLYVKRMHGSSNEAPSSSDPLFASPTVPKSSRNSVSGGGTVNPHSHVPIPMPYQPQM...

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_017843`
TK1151 ID	TkA08G046040
OH-1004 ID	LXL04_017843
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 93.691 / OH-1004 90.549 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_017843

Location Chr04:2259071-2260390 (-)

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
`At4g16110`	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'.	The response regulator ARR2: a pollen-specific transcription factor involved in the expression of nuclear genes for components of mitochondrial complex I in Arabidopsis.2001 · DOI: 10.1007/s004380000400 Two-component circuitry in Arabidopsis cytokinin signal transduction.2001 · DOI: 10.1038/35096500 The response regulator 2 mediates ethylene signalling and hormone signal integration in Arabidopsis.2004 · DOI: 10.1038/sj.emboj.7600337 Cytokinin-mediated control of leaf longevity by AHK3 through phosphorylation of ARR2 in Arabidopsis.2006 · DOI: 10.1073/pnas.0505150103

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0971800`	Transcription factor that is essential for the generation of the circadian clock oscillation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017843 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II 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:0009723 response to ethylene Biological Process

GO:0009735 response to cytokinin Biological Process

GO:0009736 cytokinin-activated signaling pathway Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010082 regulation of root meristem growth Biological Process

GO:0010119 regulation of stomatal movement Biological Process

KEGG gene cross-reference

ath:AT2G40970

ath:AT3G46640

ath:AT4G16110

ath:AT5G59570

dosa:Os01g0971800

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.

Nucleus0.978

Rank 1 · LXL04_017843 · OH-1004

Cytoplasm0.090

Rank 2 · LXL04_017843 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_017843 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_017843 · OH-1004

Plastid0.009

Rank 5 · LXL04_017843 · 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.

PF00249.38Myb_DNA-binding155-204 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017843	`PF00249.38`	Myb_DNA-binding	155	204	2.7e-08	34.5

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	51.678%	Swiss-Prot	strong database homology
`Q9LTH4`	Arabidopsis thaliana	Transcription factor BOA	50.394%	Swiss-Prot	strong database homology
`O22210`	Arabidopsis thaliana	Transcription factor MYBC1	64.516%	Swiss-Prot	weak database homology
`Q9ZWJ9`	Arabidopsis thaliana	Two-component response regulator ARR2	56.944%	Swiss-Prot	weak database homology
`Q94DH3`	Oryza sativa subsp. japonica	Transcription factor PCL1	82.143%	Swiss-Prot	weak database homology

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