LXL04_022535 | RubberDandelionOmics

Gene overview

LXL04_022535

Reference: OH-1004 Chr: Chr05 Coordinates: 669834-672551 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1542 bp · LXL04_022535|LXL04_022535|OH1004|cDNA

ATGGACCCCTACTCATCGTCTGGAGAAATATTGAACATAAAGACAAGAAAACCGTATACAATAACAAAACAAAGAGAACGATGGACAGAAGAAGAGCATAATAGTTTTTTAGAAGCCCTGAAACTATATGGGAGAGCTTGGCAACGGATAGAAGAACACATAGGAACGAAGACCGCAGTGCAAATCAGAAGTCATGCCCAGAAGTTCTTTACAAAGCTGGAGAAGGAGGCTGTTGCTAAAGGAGTTCCAACAAGACAAGC...

CDS

Download CDS FASTA

1542 bp · LXL04_022535|LXL04_022535|OH1004|CDS

ATGGACCCCTACTCATCGTCTGGAGAAATATTGAACATAAAGACAAGAAAACCGTATACAATAACAAAACAAAGAGAACGATGGACAGAAGAAGAGCATAATAGTTTTTTAGAAGCCCTGAAACTATATGGGAGAGCTTGGCAACGGATAGAAGAACACATAGGAACGAAGACCGCAGTGCAAATCAGAAGTCATGCCCAGAAGTTCTTTACAAAGCTGGAGAAGGAGGCTGTTGCTAAAGGAGTTCCAACAAGACAAGC...

Protein

Download Protein FASTA

513 aa · LXL04_022535|LXL04_022535|OH1004|PROTEIN

MDPYSSSGEILNIKTRKPYTITKQRERWTEEEHNSFLEALKLYGRAWQRIEEHIGTKTAVQIRSHAQKFFTKLEKEAVAKGVPTRQALDMEIPPPRPKRKPNYPYPRKSHQPSLKPIPDPQTTTHEHGDEHEENAKTNEEMEKKEMSCASLSSENENNSRELMKNLDETNKSYITTDQCQNPRGGNYPRHVHVQVVDGSQGVITGEEESTVNIASCSSYPPAFPFTPFSDNQFLHVSSTISSLIVSSLLQNPAAHAAATF...

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_022535`
TK1151 ID	TkA06G477730
OH-1004 ID	LXL04_022535
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	78.800
Protein coverage (%)	TK1151 51.212 / OH-1004 27.875 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_022535

Location Chr05:669834-672551 (-)

Description Similar to LHY: Protein LHY

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g01060`	Transcription factor involved in the circadian clock.	No verified direct reference in this release
`At2g46830`	Transcription factor involved in the circadian clock and in the phytochrome regulation.	Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock.2001 · DOI: 10.1126/science.1061320 Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis.2002 · DOI: 10.1016/s0960-9822(02)00815-1 LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis.2002 · DOI: 10.1016/s1534-5807(02)00170-3 The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots.2008 · DOI: 10.1126/science.1161403 CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis.2009 · DOI: 10.1104/pp.108.133272 Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis.2009 · DOI: 10.1104/pp.109.137414 FBH1 affects warm temperature responses in the Arabidopsis circadian clock.2014 · DOI: 10.1073/pnas.1416666111 Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis.2019 · DOI: 10.1186/s13059-019-1777-1 Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression.1998 · DOI: 10.1016/s0092-8674(00)81464-6
`At5g37260`	Positive regulator for cold-responsive gene expression and cold tolerance.	Constitutive expression of CIR1 (RVE2) affects several circadian-regulated processes and seed germination in Arabidopsis.2007 · DOI: 10.1111/j.1365-313x.2007.03156.x A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis.2013 · DOI: 10.1105/tpc.112.108340

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0157600`	Transcription factor involved in the regulation of tiller growth and panicle development.	The Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing.2020 · DOI: 10.1105/tpc.20.00289 Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance.2022 · DOI: 10.1093/plphys/kiac196

Functional annotation source

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Functional annotation source: OH1004 · LXL04_022535 · 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:0009408 response to heat Biological Process

GO:0009409 response to cold Biological Process

GO:0010378 temperature compensation of the circadian clock Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010597 green leaf volatile biosynthetic process Biological Process

GO:0042752 regulation of circadian rhythm Biological Process

GO:0042754 negative regulation of circadian rhythm Biological Process

GO:0043254 regulation of protein-containing complex assembly Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT1G01060

ath:AT2G46830

dosa:Os08g0157600

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.

Nucleus0.974

Rank 1 · LXL04_022535 · OH-1004

Cytoplasm0.086

Rank 2 · LXL04_022535 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_022535 · OH-1004

Endoplasmic reticulum0.011

Rank 4 · LXL04_022535 · OH-1004

Plastid0.009

Rank 5 · LXL04_022535 · 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-binding25-68 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022535	`PF00249.38`	Myb_DNA-binding	25	68	2.5e-13	50.6

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
`Q6R0H1`	Arabidopsis thaliana	Protein LHY	40.280%	Swiss-Prot	moderate database homology
`P92973`	Arabidopsis thaliana	Protein CCA1	39.839%	Swiss-Prot	moderate database homology
`F4K5X6`	Arabidopsis thaliana	Protein REVEILLE 2	62.295%	Swiss-Prot	weak database homology
`A0A0P0XBU0`	Oryza sativa subsp. japonica	Protein CCA1	81.731%	Swiss-Prot	weak database homology

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