LXL04_021037 | RubberDandelionOmics

Gene overview

LXL04_021037

Reference: OH-1004 Chr: Chr04 Coordinates: 119482836-119484143 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1308 bp · LXL04_021037|LXL04_021037|OH1004|cDNA

ATGGAAATATattcttctgcttcttcttttgAAACTAATCTTACACTCCAAACGCAAAATAGCTTTCGAGATGCTTCTTTCTCATCCTATTTGAATAAAGCTGAAGAAAACATGATTCGAAAGCTCACTAATCAAGCATCAGATAGCGCAAAGGATCACAAGCATCCACTTCGTAAGAAATCCGAAGACGAAGAAATTGGCGTTTTTGGTGCGGAAAAGTACTTTACAGAGGAAATTGAAGATGGGGATAATAAGAATGG...

CDS

Download CDS FASTA

1308 bp · LXL04_021037|LXL04_021037|OH1004|CDS

ATGGAAATATATTCTTCTGCTTCTTCTTTTGAAACTAATCTTACACTCCAAACGCAAAATAGCTTTCGAGATGCTTCTTTCTCATCCTATTTGAATAAAGCTGAAGAAAACATGATTCGAAAGCTCACTAATCAAGCATCAGATAGCGCAAAGGATCACAAGCATCCACTTCGTAAGAAATCCGAAGACGAAGAAATTGGCGTTTTTGGTGCGGAAAAGTACTTTACAGAGGAAATTGAAGATGGGGATAATAAGAATGG...

Protein

Download Protein FASTA

435 aa · LXL04_021037|LXL04_021037|OH1004|PROTEIN

MEIYSSASSFETNLTLQTQNSFRDASFSSYLNKAEENMIRKLTNQASDSAKDHKHPLRKKSEDEEIGVFGAEKYFTEEIEDGDNKNGRRFLHTTNLGSMMYQKTETIEELNRCISAKQTTDDLNMHTPSVRSNVSCNSRSGLLPRMMQAPGKSQKGSKSKLFLARFGCNCIDKKSTQINEKKFIQAKGISNKKTDLLSSKLAEKNTRNDYFSFPVLNSNEHSPNWSSNSKSGNLAGKIQGDKNVGRFSLGKKLTLLNDWD...

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_021037`
TK1151 ID	TkA05G344270
OH-1004 ID	LXL04_021037
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.900
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_021037

Location Chr04:119482836-119484143 (-)

Description Similar to PKS1: Protein PHYTOCHROME KINASE SUBSTRATE 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g02950`	May be responsible for light-regulated cytoplasmic sequestration of phytochromes or may be a negative regulator of phytochrome B signaling.	PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis.1999 · DOI: 10.1126/science.284.5419.1539 PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.2006 · DOI: 10.1073/pnas.0603799103 PHYTOCHROME KINASE SUBSTRATE1 regulates root phototropism and gravitropism.2008 · DOI: 10.1104/pp.107.106468 The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling element that regulates leaf flattening and leaf positioning.2010 · DOI: 10.1104/pp.109.150441
`At1g14280`	Acts predominantly in the phot1 pathway.	No verified direct reference in this release
`At1g18810`	Probably involved in the phytochrome signaling pathway.	No verified direct reference in this release
`At5g04190`	Modulates phytochrome-mediated control of hypocotyl growth orientation.	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_021037 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009611 response to wounding Biological Process

GO:0009638 phototropism Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010017 red or far-red light signaling pathway Biological Process

GO:0010114 response to red light Biological Process

GO:0010218 response to far red light Biological Process

GO:0048366 leaf development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009506 plasmodesma Cellular Component

KEGG gene cross-reference

ath:AT1G14280

ath:AT1G18810

ath:AT2G02950

ath:AT5G04190

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.

Cell membrane0.469

Rank 1 · LXL04_021037 · OH-1004

Nucleus0.373

Rank 2 · LXL04_021037 · OH-1004

Cytoplasm0.351

Rank 3 · LXL04_021037 · OH-1004

Endoplasmic reticulum0.051

Rank 4 · LXL04_021037 · OH-1004

Plastid0.034

Rank 5 · LXL04_021037 · 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.

PF30823.1PKS276-386 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021037	`PF30823.1`	PKS	276	386	3.8e-11	43.4

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
`Q9SWI1`	Arabidopsis thaliana	Protein PHYTOCHROME KINASE SUBSTRATE 1	32.873%	Swiss-Prot	moderate database homology
`Q9M9T4`	Arabidopsis thaliana	Protein PHYTOCHROME KINASE SUBSTRATE 2	31.536%	Swiss-Prot	moderate database homology
`Q8GXS8`	Arabidopsis thaliana	Protein PHYTOCHROME KINASE SUBSTRATE 3	26.891%	Swiss-Prot	weak database homology
`Q9FYE2`	Arabidopsis thaliana	Protein PHYTOCHROME KINASE SUBSTRATE 4	26.969%	Swiss-Prot	weak database homology

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