LXL04_021542 | RubberDandelionOmics

Gene overview

LXL04_021542

Reference: OH-1004 Chr: Chr04 Coordinates: 132180618-132181091 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

474 bp · LXL04_021542|LXL04_021542|OH1004|cDNA

ATGGATCCAACAAACAACTCATCatcgtcttcatcttctccaagTCGATACGAGAGCCAGAAACGTAGAGACTGGGATACATTTGGTCAGTACTTAAGAAACAACAAGCCACCACTTTCTTTCGCTCACTTTAACCCTAGTCATGTTCTTGAGTTTCTTCACTATCTTGATCAATTCGGAAAGACGAAAATCCACATCTTGACATGCCCTTACTTCGGAGTACCAAACCCACCGACAGCTTGCCCTTGTCCTTTCCGGCA...

CDS

Download CDS FASTA

474 bp · LXL04_021542|LXL04_021542|OH1004|CDS

ATGGATCCAACAAACAACTCATCATCGTCTTCATCTTCTCCAAGTCGATACGAGAGCCAGAAACGTAGAGACTGGGATACATTTGGTCAGTACTTAAGAAACAACAAGCCACCACTTTCTTTCGCTCACTTTAACCCTAGTCATGTTCTTGAGTTTCTTCACTATCTTGATCAATTCGGAAAGACGAAAATCCACATCTTGACATGCCCTTACTTCGGAGTACCAAACCCACCGACAGCTTGCCCTTGTCCTTTCCGGCA...

Protein

Download Protein FASTA

157 aa · LXL04_021542|LXL04_021542|OH1004|PROTEIN

MDPTNNSSSSSSSPSRYESQKRRDWDTFGQYLRNNKPPLSFAHFNPSHVLEFLHYLDQFGKTKIHILTCPYFGVPNPPTACPCPFRQAWGSLDALVGRLRAAYDEHGGNPETNPFGAPEVRRFLREVRDFQAKSRGISYEKKRKRPKQKQQEDRQQE

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_021542`
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_021542

Location Chr04:132180618-132181091 (+)

Description Similar to LSH6: Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At5g58500`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At3g04510`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`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
`At5g28490`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to continuous red (cR), far-red (cFR) and blue (cB) light in a phytochrome-dependent manner, at least during seedling development.	Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development.2004 · DOI: 10.1111/j.1365-313x.2003.01993.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021542 · 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:0009637 response to blue light Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0010114 response to red light Biological Process

GO:0010218 response to far red light Biological Process

GO:0090698 post-embryonic plant morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G07090

ath:AT2G42610

ath:AT3G04510

ath:AT5G28490

ath:AT5G58500

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.

Nucleus0.864

Rank 1 · LXL04_021542 · OH-1004

Cytoplasm0.239

Rank 2 · LXL04_021542 · OH-1004

Mitochondrion0.039

Rank 3 · LXL04_021542 · OH-1004

Cell membrane0.019

Rank 4 · LXL04_021542 · OH-1004

Endoplasmic reticulum0.016

Rank 5 · LXL04_021542 · 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_dom9-129 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021542	`PF04852.18`	ALOG_dom	9	129	1.4e-58	197.3

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
`Q9LMK2`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6	67.143%	Swiss-Prot	strong database homology
`Q9FGH2`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 5	68.889%	Swiss-Prot	strong database homology
`Q9M836`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 2	73.333%	Swiss-Prot	strong database homology
`Q9S7R3`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 10	62.963%	Swiss-Prot	strong database homology
`Q6NNI3`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 1	66.443%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card