LXL04_016619 | RubberDandelionOmics

Gene overview

LXL04_016619

Reference: OH-1004 Chr: Chr03 Coordinates: 129358962-129363436 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

948 bp · LXL04_016619|LXL04_016619|OH1004|cDNA

ATGTCTAGTGATCACCAGATTACGGGAAGATCCGAAATAGGTGAAGGATCATCATCAAGAGGTGGcggaggtggaggtggtggtggtggtgttgtTGTATCAGCGCCGGCACCACCACAACAACTAAGCCGATACGAATCACAGAAGCGGCGTGACTGGAACACGTTTGGGCAGTACTTGAAGAACCAACGACCACCAGTGGCGTTGTCTCACTGCAGCTACAGTCATGTACTAGATTTCCTTCGGTACCTCGATCAGTT...

CDS

Download CDS FASTA

948 bp · LXL04_016619|LXL04_016619|OH1004|CDS

ATGTCTAGTGATCACCAGATTACGGGAAGATCCGAAATAGGTGAAGGATCATCATCAAGAGGTGGCGGAGGTGGAGGTGGTGGTGGTGGTGTTGTTGTATCAGCGCCGGCACCACCACAACAACTAAGCCGATACGAATCACAGAAGCGGCGTGACTGGAACACGTTTGGGCAGTACTTGAAGAACCAACGACCACCAGTGGCGTTGTCTCACTGCAGCTACAGTCATGTACTAGATTTCCTTCGGTACCTCGATCAGTT...

Protein

Download Protein FASTA

315 aa · LXL04_016619|LXL04_016619|OH1004|PROTEIN

MSSDHQITGRSEIGEGSSSRGGGGGGGGGGVVVSAPAPPQQLSRYESQKRRDWNTFGQYLKNQRPPVALSHCSYSHVLDFLRYLDQFGKTKVHLQGCVFFGHPDPAGPCTCPLRQAWGSLDALIGRLRAAYEENGGLPEMNPFASGAIRVYLREIRDSQAKARGIPYKKKKKKKNTPIMKANEETSMFESFENLYISRTSRTPPIFYISQTVIHFKKPTSIPSKTTSIKFETYTYAKKQNCKICTYAKTPKPLNFSKNQI...

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_016619`
TK1151 ID	TkA02G117290
OH-1004 ID	LXL04_016619
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	96.800
Protein coverage (%)	TK1151 76.113 / OH-1004 59.683 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_016619

Location Chr03:129358962-129363436 (+)

Description Similar to LSH10: Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 10

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g42610`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At1g07090`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At1g78815`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At4g18610`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At1g16910`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_016619 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009299 mRNA transcription Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0090698 post-embryonic plant morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G07090

ath:AT1G16910

ath:AT1G78815

ath:AT2G42610

ath:AT4G18610

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.

Nucleus0.623

Rank 1 · LXL04_016619 · OH-1004

Cytoplasm0.308

Rank 2 · LXL04_016619 · OH-1004

Mitochondrion0.081

Rank 3 · LXL04_016619 · OH-1004

Cell membrane0.036

Rank 4 · LXL04_016619 · OH-1004

Endoplasmic reticulum0.032

Rank 5 · LXL04_016619 · 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.

PF04852.18ALOG_dom35-157 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016619	`PF04852.18`	ALOG_dom	35	157	3.2e-65	218.7

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
`Q9S7R3`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 10	80.795%	Swiss-Prot	weak database homology
`Q9LMK2`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6	70.199%	Swiss-Prot	weak database homology
`Q9ZVA0`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 7	75.352%	Swiss-Prot	weak database homology
`Q9SN52`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 9	79.365%	Swiss-Prot	weak database homology
`Q9FZ51`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 8	71.324%	Swiss-Prot	weak database homology

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