LXL04_000293 | RubberDandelionOmics

Gene overview

LXL04_000293

Reference: OH-1004 Chr: Chr01 Coordinates: 5526134-5529518 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1389 bp · LXL04_000293|LXL04_000293|OH1004|cDNA

ATGCTAGCTTTATCCCCAACGCAGTTCTCACCTATTTACGGATGGCCCTCAGAGGATCTTATCCAACAGGAATGCAATGATATTTCTATAGAAGCTGAAGCAAATTCACATAAATCGTTTCTTGATTTTCATACATATAATGATATCCATCAAGATTCTGCAACTGAAATTTACTCTTTTTCTGGGGAGGTTGCAAATGGCGATTTCAGTAATCCTATGTTGAAAAAGCTCAATCATAATGCTAGTGAAAGAGATCGTCG...

CDS

Download CDS FASTA

1389 bp · LXL04_000293|LXL04_000293|OH1004|CDS

ATGCTAGCTTTATCCCCAACGCAGTTCTCACCTATTTACGGATGGCCCTCAGAGGATCTTATCCAACAGGAATGCAATGATATTTCTATAGAAGCTGAAGCAAATTCACATAAATCGTTTCTTGATTTTCATACATATAATGATATCCATCAAGATTCTGCAACTGAAATTTACTCTTTTTCTGGGGAGGTTGCAAATGGCGATTTCAGTAATCCTATGTTGAAAAAGCTCAATCATAATGCTAGTGAAAGAGATCGTCG...

Protein

Download Protein FASTA

462 aa · LXL04_000293|LXL04_000293|OH1004|PROTEIN

MLALSPTQFSPIYGWPSEDLIQQECNDISIEAEANSHKSFLDFHTYNDIHQDSATEIYSFSGEVANGDFSNPMLKKLNHNASERDRRKRVNDLYAFLRSVLPNSSDQKKKISIPGTVSRALKYIPELQKEVATLIRKKEKLSLDSSSKYDLRQQGMKNKIGKDAKIETKSSVVSSVKVLGAKEAVIQLISLNDHMSKTKKIGLLSKVMEYLEKEEDIVLINSTTFKCFGEGMSLLSTLHIQVNGENSIDAERLKEKLCSF...

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_000293`
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_000293

Location Chr01:5526134-5529518 (+)

Description Similar to ORG2: Transcription factor ORG2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g56970`	Transcription factor ORG2.	No verified direct reference in this release
`At2g41240`	Plays a role in metal homeostasis.	Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd-hyperaccumulator Thlaspi caerulescens.2008 · DOI: 10.1111/j.1365-3040.2007.01764.x
`At3g56980`	Transcription factor ORG3.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2WZ60`	Transcription activator that binds to the DNA motif 5'-CACGTGG-3' in the promoter of iron (Fe) deficiency-inducible genes as well as of genes involved in iron homeostasis, thus contributing to basal tolerance to iron deficiency, iron uptake from soil and iron transport, particularly during seed maturation and germination.	No verified direct reference in this release
`Os01g0952800`	Transcription activator that binds to the DNA motif 5'-CACGTGG-3' in the promoter of iron (Fe) deficiency-inducible genes as well as of genes involved in iron homeostasis, thus contributing to basal tolerance to iron deficiency, iron uptake from soil and iron transport, particularly during seed maturation and germination.	Isolation and characterization of IRO2, a novel iron-regulated bHLH transcription factor in graminaceous plants.2006 · DOI: 10.1093/jxb/erl054 The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions.2007 · DOI: 10.1111/j.1365-313x.2007.03149.x Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa.2011 · DOI: 10.1093/jxb/erq301 OsIRO2 is responsible for iron utilization in rice and improves growth and yield in calcareous soil.2011 · DOI: 10.1007/s11103-011-9752-6 Iron deficiency responses in rice roots.2014 · DOI: 10.1186/s12284-014-0027-0

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000293 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0010104 regulation of ethylene-activated signaling pathway Biological Process

GO:0010106 cellular response to iron ion starvation Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0046685 response to arsenic-containing substance Biological Process

GO:0046686 response to cadmium ion Biological Process

GO:0060586 multicellular organismal-level iron ion homeostasis Biological Process

KEGG gene cross-reference

ath:AT2G41240

ath:AT3G56970

ath:AT3G56980

dosa:Os01g0952800

osa:4325750

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.

Nucleus0.856

Rank 1 · LXL04_000293 · OH-1004

Cytoplasm0.186

Rank 2 · LXL04_000293 · OH-1004

Cell membrane0.061

Rank 3 · LXL04_000293 · OH-1004

Endoplasmic reticulum0.050

Rank 4 · LXL04_000293 · OH-1004

Plastid0.017

Rank 5 · LXL04_000293 · 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.

PF00010.32HLH75-128 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000293	`PF00010.32`	HLH	75	128	5.9e-12	45.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9M1K1`	Arabidopsis thaliana	Transcription factor ORG2	35.165%	Swiss-Prot	moderate database homology
`Q9ZVB5`	Arabidopsis thaliana	Transcription factor bHLH100	34.815%	Swiss-Prot	moderate database homology
`Q9M1K0`	Arabidopsis thaliana	Transcription factor ORG3	36.042%	Swiss-Prot	moderate database homology
`A2WZ60`	Oryza sativa subsp. indica	Protein IRON-RELATED TRANSCRIPTION FACTOR 2	38.983%	Swiss-Prot	weak database homology
`Q0JFZ0`	Oryza sativa subsp. japonica	Protein IRON-RELATED TRANSCRIPTION FACTOR 2	37.853%	Swiss-Prot	weak database homology

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