LXL04_000934 | RubberDandelionOmics

Gene overview

LXL04_000934

Reference: OH-1004 Chr: Chr01 Coordinates: 16864689-16865288 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

600 bp · LXL04_000934|LXL04_000934|OH1004|cDNA

ATGAATCTTTACCCGGAGGTGGAAAGCTGCAACAACTCGGATAACAGTCATCACGCTATCAGCAATTTGGTCACCGCCGCATCTGCATCTTCGCCATCAATCAACTCCACTCCAAGCCGCTATGAGAACCAAAAGCGTCGAGACTGGAACACGTTTGGTCAGTACTTGAAGAACCACCGTCCGCCTCTTTCACTCTCCCGGTGTAGTGGGGCCCATGTTCTTGAATTCCTCCGGTACCTCGATCAGTTTGGAAAGACTAA...

CDS

Download CDS FASTA

600 bp · LXL04_000934|LXL04_000934|OH1004|CDS

ATGAATCTTTACCCGGAGGTGGAAAGCTGCAACAACTCGGATAACAGTCATCACGCTATCAGCAATTTGGTCACCGCCGCATCTGCATCTTCGCCATCAATCAACTCCACTCCAAGCCGCTATGAGAACCAAAAGCGTCGAGACTGGAACACGTTTGGTCAGTACTTGAAGAACCACCGTCCGCCTCTTTCACTCTCCCGGTGTAGTGGGGCCCATGTTCTTGAATTCCTCCGGTACCTCGATCAGTTTGGAAAGACTAA...

Protein

Download Protein FASTA

199 aa · LXL04_000934|LXL04_000934|OH1004|PROTEIN

MNLYPEVESCNNSDNSHHAISNLVTAASASSPSINSTPSRYENQKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHSPICPFYGHPDPPAPCPCPLRQAWGSLDALIGRLRAAYEENGWPPETNPFGARAVRLYLREVRDLQSKARGISYEKKKRKRGPTHEHHHHQLPSFSTFQALPLPPGDHRI

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_000934`
TK1151 ID	TkA01G575360
OH-1004 ID	LXL04_000934
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	81.900
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

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Basic Information and Functional Annotation

Gene ID LXL04_000934

Location Chr01:16864689-16865288 (+)

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

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g31160`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity).	Organ boundary1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs.2011 · DOI: 10.1073/pnas.1018542108
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0811000`	Transcription factor required for lateral development of the lemma and palea.	TH1, a DUF640 domain-like gene controls lemma and palea development in rice.2012 · DOI: 10.1007/s11103-011-9868-8 Beak-shaped grain 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice.2013 · DOI: 10.1007/s11427-013-4449-5 The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height, floral development and grain yield in rice.2016 · DOI: 10.1111/jipb.12441
`UniProt: A2XAV5`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000934 · 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:0010199 organ boundary specification between lateral organs and the meristem Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048441 petal development Biological Process

GO:0048834 specification of petal number Biological Process

GO:0080050 regulation of seed development Biological Process

GO:0090698 post-embryonic plant morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0042803 protein homodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT1G07090

ath:AT2G31160

ath:AT5G58500

dosa:Os02g0811000

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.

Nucleus0.870

Rank 1 · LXL04_000934 · OH-1004

Cytoplasm0.290

Rank 2 · LXL04_000934 · OH-1004

Mitochondrion0.034

Rank 3 · LXL04_000934 · OH-1004

Cell membrane0.017

Rank 4 · LXL04_000934 · OH-1004

Endoplasmic reticulum0.013

Rank 5 · LXL04_000934 · 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_dom32-153 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000934	`PF04852.18`	ALOG_dom	32	153	2.1e-65	219.3

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
`O82268`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3	75.581%	Swiss-Prot	strong database homology
`Q9LMK2`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6	79.710%	Swiss-Prot	moderate database homology
`Q9FGH2`	Arabidopsis thaliana	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 5	76.866%	Swiss-Prot	moderate database homology
`Q6K5X1`	Oryza sativa subsp. japonica	Protein G1-like6	88.636%	Swiss-Prot	moderate database homology
`A2XAV5`	Oryza sativa subsp. indica	Protein G1-like6	88.636%	Swiss-Prot	moderate database homology

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