LXL04_021009 | RubberDandelionOmics

Gene overview

LXL04_021009

Reference: OH-1004 Chr: Chr04 Coordinates: 118660467-118662294 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1206 bp · LXL04_021009|LXL04_021009|OH1004|cDNA

ATGGAGCAACAACCAATGGATACTTCTTTTGAACAATCTATCAATAATCGGTACTCATTTTGGGTCCGAGAAGCTCTTGACGAACTCCCCCATAGTTTCACCATAACCGACCCGTCAATTTCGGGTCACCCGATTGTTTTTGCTTCAAGGGAGTTCTTGAAAATGTCTGGCTATTCAAGAGAGGAGGTGATTGGAAAGAATGGACGGATGTTTCAAGGGATTAGGACTAATAGGAGATCAGTAATGGAGATTAGGGAAGC...

CDS

Download CDS FASTA

1206 bp · LXL04_021009|LXL04_021009|OH1004|CDS

ATGGAGCAACAACCAATGGATACTTCTTTTGAACAATCTATCAATAATCGGTACTCATTTTGGGTCCGAGAAGCTCTTGACGAACTCCCCCATAGTTTCACCATAACCGACCCGTCAATTTCGGGTCACCCGATTGTTTTTGCTTCAAGGGAGTTCTTGAAAATGTCTGGCTATTCAAGAGAGGAGGTGATTGGAAAGAATGGACGGATGTTTCAAGGGATTAGGACTAATAGGAGATCAGTAATGGAGATTAGGGAAGC...

Protein

Download Protein FASTA

401 aa · LXL04_021009|LXL04_021009|OH1004|PROTEIN

MEQQPMDTSFEQSINNRYSFWVREALDELPHSFTITDPSISGHPIVFASREFLKMSGYSREEVIGKNGRMFQGIRTNRRSVMEIREAIREERSIQVSLLNYHKNGTPFWILFHMFPVFSKEDGRVIHFVGVQVPIMPKPRRSGSEFSRIEVNLYENGAGFRDTVLGFCRREVCSDTVAELGRISNLDQVLSADTELTDTACKASDLEKRRANTAMSNILSMLTHYSESMGRLVSDKRCCPHNMSRVGASLNISLGRIKQS...

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_021009`
TK1151 ID	TkA05G340150
OH-1004 ID	LXL04_021009
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_021009

Location Chr04:118660467-118662294 (+)

Description Similar to TLP1: Protein TWIN LOV 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g02710`	Protein TWIN LOV 1.	No verified direct reference in this release
`At5g58140`	Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements.	Arabidopsis NPL1: a phototropin homolog controlling the chloroplast high-light avoidance response.2001 · DOI: 10.1126/science.291.5511.2138 Arabidopsis nph1 and npl1: blue light receptors that mediate both phototropism and chloroplast relocation.2001 · DOI: 10.1073/pnas.101137598 Phot1 and phot2 mediate blue light-induced transient increases in cytosolic Ca2+ differently in Arabidopsis leaves.2003 · DOI: 10.1073/pnas.1336802100 A transgene encoding a blue-light receptor, phot1, restores blue-light responses in the Arabidopsis phot1 phot2 double mutant.2004 · DOI: 10.1093/jxb/erh044 Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis.2004 · DOI: 10.1073/pnas.0305984101 RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana.2004 · DOI: 10.1105/tpc.019901 Biochemical characterization of plasma membrane H+-ATPase activation in guard cell protoplasts of Arabidopsis thaliana in response to blue light.2005 · DOI: 10.1093/pcp/pci104 An ATP-Binding Cassette Transporter, ABCB19, Regulates Leaf Position and Morphology during Phototropin1-Mediated Blue Light Responses.2020 · DOI: 10.1104/pp.20.00223
`At3g45780`	Protein kinase that acts as a blue light (BL) photoreceptor in a signal-transduction pathway for photo-induced movements.	RPT2. A signal transducer of the phototropic response in Arabidopsis.2000 · DOI: 10.1105/tpc.12.2.225 Unexpected roles for cryptochrome 2 and phototropin revealed by high-resolution analysis of blue light-mediated hypocotyl growth inhibition.2001 · DOI: 10.1046/j.1365-313x.2001.01038.x Phototropin 1 is required for high-fluence blue-light-mediated mRNA destabilization.2003 · DOI: 10.1023/a:1022393406204 Phot1 and phot2 mediate blue light-induced transient increases in cytosolic Ca2+ differently in Arabidopsis leaves.2003 · DOI: 10.1073/pnas.1336802100 A transgene encoding a blue-light receptor, phot1, restores blue-light responses in the Arabidopsis phot1 phot2 double mutant.2004 · DOI: 10.1093/jxb/erh044 Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis.2004 · DOI: 10.1073/pnas.0305984101 RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana.2004 · DOI: 10.1105/tpc.019901 Biochemical characterization of plasma membrane H+-ATPase activation in guard cell protoplasts of Arabidopsis thaliana in response to blue light.2005 · DOI: 10.1093/pcp/pci104 PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.2006 · DOI: 10.1073/pnas.0603799103 In vivo phosphorylation site mapping and functional characterization of Arabidopsis phototropin 1.2008 · DOI: 10.1093/mp/ssm017 An ATP-Binding Cassette Transporter, ABCB19, Regulates Leaf Position and Morphology during Phototropin1-Mediated Blue Light Responses.2020 · DOI: 10.1104/pp.20.00223

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0304200`	Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for phototropic responses.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021009 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007623 circadian rhythm Biological Process

GO:0009637 response to blue light Biological Process

GO:0009638 phototropism Biological Process

GO:0009639 response to red or far red light Biological Process

GO:0009785 blue light signaling pathway Biological Process

GO:0009902 chloroplast relocation Biological Process

GO:0009903 chloroplast avoidance movement Biological Process

GO:0009904 chloroplast accumulation movement Biological Process

GO:0010118 stomatal movement Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0010155 regulation of proton transport Biological Process

GO:0046777 protein autophosphorylation Biological Process

KEGG gene cross-reference

ath:AT2G02710

ath:AT3G45780

ath:AT5G58140

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.

Cytoplasm0.381

Rank 1 · LXL04_021009 · OH-1004

Nucleus0.265

Rank 2 · LXL04_021009 · OH-1004

Cell membrane0.179

Rank 3 · LXL04_021009 · OH-1004

Mitochondrion0.118

Rank 4 · LXL04_021009 · OH-1004

Endoplasmic reticulum0.080

Rank 5 · LXL04_021009 · 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.

PF13426.14PAS_942-132 aa

PF00989.32PAS45-131 aa

PF08447.19PAS_345-131 aa

PF13426.14PAS_9260-362 aa

PF00989.32PAS273-360 aa

PF08447.19PAS_3273-356 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021009	`PF13426.14`	PAS_9	42	132	2.5e-40	137.6
LXL04_021009	`PF00989.32`	PAS	45	131	5.2e-18	65.8
LXL04_021009	`PF08447.19`	PAS_3	45	131	5.9e-17	62.4
LXL04_021009	`PF13426.14`	PAS_9	260	362	2.5e-40	137.6
LXL04_021009	`PF00989.32`	PAS	273	360	5.2e-18	65.8
LXL04_021009	`PF08447.19`	PAS_3	273	356	5.9e-17	62.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O64511`	Arabidopsis thaliana	Protein TWIN LOV 1	57.908%	Swiss-Prot	strong database homology
`P93025`	Arabidopsis thaliana	Phototropin-2	32.564%	Swiss-Prot	moderate database homology
`O48963`	Arabidopsis thaliana	Phototropin-1	30.446%	Swiss-Prot	moderate database homology
`Q9ST27`	Oryza sativa subsp. japonica	Phototropin-2	49.573%	Swiss-Prot	weak database homology

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