LXL04_016001 | RubberDandelionOmics

Gene overview

LXL04_016001

Reference: OH-1004 Chr: Chr03 Coordinates: 102907988-102913653 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2667 bp · LXL04_016001|LXL04_016001|OH1004|cDNA

ATGGAAAGTTCAGATCCGGAATCAAGCACCAAAAATAATAAATGGATGGCATTCGATAATCAAAACAAACCGCCAATCGCTAGAATCACTCCACCTGAAGATGAATATGACACGGATCACATAGCCGAACGGACAGCGGCTTGGCCGGGAGCAACAGCAGTCGCAGGGTTAATCGGGGATGAGGAGAGAAATAAGCGAAGCTCGTCGTCGTCGTGGAGGACGTCAGATGATTTGAATCATCCGCGAGTCTCGCAAGACTT...

CDS

Download CDS FASTA

2667 bp · LXL04_016001|LXL04_016001|OH1004|CDS

ATGGAAAGTTCAGATCCGGAATCAAGCACCAAAAATAATAAATGGATGGCATTCGATAATCAAAACAAACCGCCAATCGCTAGAATCACTCCACCTGAAGATGAATATGACACGGATCACATAGCCGAACGGACAGCGGCTTGGCCGGGAGCAACAGCAGTCGCAGGGTTAATCGGGGATGAGGAGAGAAATAAGCGAAGCTCGTCGTCGTCGTGGAGGACGTCAGATGATTTGAATCATCCGCGAGTCTCGCAAGACTT...

Protein

Download Protein FASTA

888 aa · LXL04_016001|LXL04_016001|OH1004|PROTEIN

MESSDPESSTKNNKWMAFDNQNKPPIARITPPEDEYDTDHIAERTAAWPGATAVAGLIGDEERNKRSSSSSWRTSDDLNHPRVSQDLKDALATLQQTFVVSDATKPDCPIMYASSGFFTMTGYSSKEVIGRNCRFLQGKETDQKEVDKIRNAVKTGTSYCGRLYNYKKDGTPFWNLLTVTPIKDENGKTIKFIGMQVEVSKYTEGVNDKELRPNGLPTSLIRYDARQKETALGSIVEVVQTVERPRTNNQSSKTETVERI...

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_016001`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_016001

Location Chr03:102907988-102913653 (-)

Description Similar to PHOT2: Phototropin-2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`Os12g0101800`	Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for phototropic responses.	No verified direct reference in this release
`Os11g0102200`	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_016001 · 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:AT3G45780

ath:AT5G58140

dosa:Os04g0304200

dosa:Os11g0102200

dosa:Os12g0101800

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.

Cytoplasm0.511

Rank 1 · LXL04_016001 · OH-1004

Cell membrane0.405

Rank 2 · LXL04_016001 · OH-1004

Nucleus0.280

Rank 3 · LXL04_016001 · OH-1004

Golgi apparatus0.046

Rank 4 · LXL04_016001 · OH-1004

Endoplasmic reticulum0.040

Rank 5 · LXL04_016001 · 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.

PF13426.14PAS_9104-200 aa

PF00989.32PAS110-195 aa

PF08447.19PAS_3110-194 aa

PF13426.14PAS_9377-469 aa

PF00989.32PAS380-469 aa

PF08447.19PAS_3381-466 aa

PF00069.32Pkinase557-841 aa

PF07714.24PK_Tyr_Ser-Thr559-803 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016001	`PF13426.14`	PAS_9	104	200	7.3e-44	149.0
LXL04_016001	`PF00989.32`	PAS	110	195	1.6e-18	67.5
LXL04_016001	`PF08447.19`	PAS_3	110	194	3.8e-17	63.1
LXL04_016001	`PF13426.14`	PAS_9	377	469	7.3e-44	149.0
LXL04_016001	`PF00989.32`	PAS	380	469	1.6e-18	67.5
LXL04_016001	`PF08447.19`	PAS_3	381	466	3.8e-17	63.1
LXL04_016001	`PF00069.32`	Pkinase	557	841	1.1e-59	202.7
LXL04_016001	`PF07714.24`	PK_Tyr_Ser-Thr	559	803	2.4e-24	86.8

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
`P93025`	Arabidopsis thaliana	Phototropin-2	70.412%	Swiss-Prot	strong database homology
`O48963`	Arabidopsis thaliana	Phototropin-1	62.303%	Swiss-Prot	strong database homology
`Q9ST27`	Oryza sativa subsp. japonica	Phototropin-2	68.277%	Swiss-Prot	strong database homology
`Q2QYY8`	Oryza sativa subsp. japonica	Phototropin-1A	59.771%	Swiss-Prot	strong database homology
`Q2RBR1`	Oryza sativa subsp. japonica	Phototropin-1B	59.657%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card