LXL04_012651 | RubberDandelionOmics

Gene overview

LXL04_012651

Reference: OH-1004 Chr: Chr03 Coordinates: 16278011-16280305 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

939 bp · LXL04_012651|LXL04_012651|OH1004|cDNA

ATGAGCAATCCGAATAAAATTTCTACGCATTCGTCGTCATCATTAATGGCGGCAAATTCGACGCCGACGGATAGTTCTGGGAAGAAGGTACGGAAGCCCTATACTATTACCAAGTCCAGAGAGAGTTGGACCGAAGAAGAACACGATAAGTTCCTTGAAGCACTTCAACTATTTGATCGTGACTGGAAGAAAATCGAAGACTTTGTTGGTTCCAAGACAGTAATTCAGATAAGAAGCCATGCCCAAAAGTACTTCCTAAA...

CDS

Download CDS FASTA

939 bp · LXL04_012651|LXL04_012651|OH1004|CDS

ATGAGCAATCCGAATAAAATTTCTACGCATTCGTCGTCATCATTAATGGCGGCAAATTCGACGCCGACGGATAGTTCTGGGAAGAAGGTACGGAAGCCCTATACTATTACCAAGTCCAGAGAGAGTTGGACCGAAGAAGAACACGATAAGTTCCTTGAAGCACTTCAACTATTTGATCGTGACTGGAAGAAAATCGAAGACTTTGTTGGTTCCAAGACAGTAATTCAGATAAGAAGCCATGCCCAAAAGTACTTCCTAAA...

Protein

Download Protein FASTA

312 aa · LXL04_012651|LXL04_012651|OH1004|PROTEIN

MSNPNKISTHSSSSLMAANSTPTDSSGKKVRKPYTITKSRESWTEEEHDKFLEALQLFDRDWKKIEDFVGSKTVIQIRSHAQKYFLKVQKNGSIAHVPPPRPKRKATHPYPQKAPKNVLLPLQASLGFPSSLSGLTPGYSPWDETSLLMSPSGRILPPQDEYDLHGFEGMHASDSGSKGTGISSGIGSSSREMPSSELSKQGEQGIPDFSEVYSFIGSVFDPETKGHVQKLKEMDPINFETVLLLMRNLTVNLSSPDFEP...

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_012651`
TK1151 ID	TkA02G547190
OH-1004 ID	LXL04_012651
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.300
Protein coverage (%)	TK1151 97.924 / OH-1004 90.705 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012651

Location Chr03:16278011-16280305 (+)

Description Similar to RVE8: Protein REVEILLE 8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g09600`	Transcriptional activator of evening element (EE)-containing clock-controlled genes.	Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation.2011 · DOI: 10.1111/j.1365-313x.2011.04484.x Histone acetylation and the circadian clock: a role for the MYB transcription factor RVE8/LCL5.2011 · DOI: 10.4161/psb.6.4.14837 REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock.2011 · DOI: 10.1371/journal.pgen.1001350 Accurate timekeeping is controlled by a cycling activator in Arabidopsis.2013 · DOI: 10.7554/elife.00473 SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively Regulates Seedling Photomorphogenesis in Arabidopsis .2022 · DOI: 10.3389/fpls.2022.836519
`At5g02840`	Probable transcription factor.	Multifocal two-photon laser scanning microscopy combined with photo-activatable GFP for in vivo monitoring of intracellular protein dynamics in real time.2007 · DOI: 10.1016/j.jsb.2006.12.012
`At5g52660`	Probable transcription factor (By similarity).	No verified direct reference in this release
`At1g01520`	Probable transcription factor.	No verified direct reference in this release
`At4g01280`	Probable transcription factor.	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_012651 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009637 response to blue light Biological Process

GO:0010099 regulation of photomorphogenesis Biological Process

GO:0010114 response to red light Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0032922 circadian regulation of gene expression Biological Process

GO:0042752 regulation of circadian rhythm Biological Process

GO:0042753 positive regulation of circadian rhythm Biological Process

GO:0043153 entrainment of circadian clock by photoperiod Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

KEGG gene cross-reference

ath:AT1G01520

ath:AT3G09600

ath:AT4G01280

ath:AT5G02840

ath:AT5G52660

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

Open Annotation Module

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.

Nucleus0.958

Rank 1 · LXL04_012651 · OH-1004

Cytoplasm0.121

Rank 2 · LXL04_012651 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_012651 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_012651 · OH-1004

Plastid0.012

Rank 5 · LXL04_012651 · 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-binding40-85 aa

PF24904.2RVE6206-268 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012651	`PF00249.38`	Myb_DNA-binding	40	85	8.9e-13	48.9
LXL04_012651	`PF24904.2`	RVE6	206	268	4.9e-36	123.4

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
`Q8RWU3`	Arabidopsis thaliana	Protein REVEILLE 8	68.750%	Swiss-Prot	strong database homology
`Q6R0G4`	Arabidopsis thaliana	Protein REVEILLE 4	66.667%	Swiss-Prot	strong database homology
`Q8H0W3`	Arabidopsis thaliana	Protein REVEILLE 6	56.349%	Swiss-Prot	strong database homology
`Q6R0H0`	Arabidopsis thaliana	Protein REVEILLE 3	55.118%	Swiss-Prot	strong database homology
`C0SVG5`	Arabidopsis thaliana	Protein REVEILLE 5	50.549%	Swiss-Prot	strong database homology

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