LXL04_038514 | RubberDandelionOmics

Gene overview

LXL04_038514

Reference: OH-1004 Chr: Chr09 Coordinates: 42881611-42882798 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

643 bp · LXL04_038514|LXL04_038514|OH1004|cDNA

ATGGCGGCATCATCCATCTCTCTATCACCAGCGTCATCATCTCGGCTCTCTCCAACCATTTCTCGGCCACGATCACCACAACATCTCTCCTTCTCTTCCTATACCTTCATCCCCACATTTCGGCTTCAACCTCATGGTCACCGTCTCCAAGCTACTCGCCGTCCTCAAAATTTCTCTCAGTTGGATTGACCAGGAAGGTGAGAATCCGGCGGCGGATCCTCGGATATGGAATCGGAATCGTAACGATATGACTTTTTCCG...

CDS

Download CDS FASTA

510 bp · LXL04_038514|LXL04_038514|OH1004|CDS

ATGGTCACCGTCTCCAAGCTACTCGCCGTCCTCAAAATTTCTCTCAGTTGGATTGACCAGGAAGGTGAGAATCCGGCGGCGGATCCTCGGATATGGAATCGGAATCGTAACGATATGACTTTTTCCGGAGATTACGATGAAGACGATGACGAAGATGATGATGAGGAGGAAGATGACAGGAGCATGGATCTTCTAATTAGGTTTGTTGAGAACGTTTTTAAGAAGATTTCTAAGCGAGCTCGCAAAGCCGTTCGATCCGT...

Protein

Download Protein FASTA

169 aa · LXL04_038514|LXL04_038514|OH1004|PROTEIN

MVTVSKLLAVLKISLSWIDQEGENPAADPRIWNRNRNDMTFSGDYDEDDDEDDDEEEDDRSMDLLIRFVENVFKKISKRARKAVRSVLPINIPTKLVGFSVNGVIILAFFWILKAFLEVVCTLGSVVFVSILLVRGVWTGISYFQEGDYRRTNDFDDGNQAWNGTQPAG

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_038514`
TK1151 ID	TkA04G437510
OH-1004 ID	LXL04_038514
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.600
Protein coverage (%)	TK1151 62.437 / OH-1004 72.781 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_038514

Location Chr09:42881611-42882798 (+)

Description Similar to SHW1: Protein SHORT HYPOCOTYL IN WHITE LIGHT 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g69935`	Negative regulator of photomorphogenesis modulating both light and abscisic acid (ABA) signaling pathways.	SHORT HYPOCOTYL IN WHITE LIGHT1, a serine-arginine-aspartate-rich protein in Arabidopsis, acts as a negative regulator of photomorphogenic growth.2008 · DOI: 10.1104/pp.108.118174 SHW1, a common regulator of abscisic acid (ABA) and light signaling pathways.2008 · DOI: 10.4161/psb.3.10.6038 Short Hypocotyl in White Light1 Interacts with Elongated Hypocotyl5 (HY5) and Constitutive Photomorphogenic1 (COP1) and Promotes COP1-Mediated Degradation of HY5 during Arabidopsis Seedling Development.2015 · DOI: 10.1104/pp.15.01184

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038514 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009416 response to light stimulus Biological Process

GO:0009642 response to light intensity Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009787 regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010380 regulation of chlorophyll biosynthetic process Biological Process

GO:0031540 regulation of anthocyanin biosynthetic process Biological Process

GO:0048578 positive regulation of long-day photoperiodism, flowering Biological Process

GO:0090227 regulation of red or far-red light signaling pathway Biological Process

GO:1901333 positive regulation of lateral root development Biological Process

KEGG gene cross-reference

ath:AT1G69935

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.

Endoplasmic reticulum0.228

Rank 1 · LXL04_038514 · OH-1004

Golgi apparatus0.178

Rank 2 · LXL04_038514 · OH-1004

Cytoplasm0.138

Rank 3 · LXL04_038514 · OH-1004

Plastid0.138

Rank 4 · LXL04_038514 · OH-1004

Lysosome / Vacuole0.118

Rank 5 · LXL04_038514 · 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.

PF28670.1SHW1_helical50-168 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038514	`PF28670.1`	SHW1_helical	50	168	1.4e-52	177.3

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
`F4I3V6`	Arabidopsis thaliana	Protein SHORT HYPOCOTYL IN WHITE LIGHT 1	49.412%	Swiss-Prot	moderate database homology

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