LXL04_010109 | RubberDandelionOmics

Gene overview

LXL04_010109

Reference: OH-1004 Chr: Chr02 Coordinates: 140311649-140313031 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

726 bp · LXL04_010109|LXL04_010109|OH1004|cDNA

ATGGTTGCCCCTGAAGACGATGATAATTCCAATTGTTTCCTCGATTATAGCTTAATCGAGCAGATTCCAGTCCCCGGAGGCGAACTTCCGTATCTTGAATCGGATTTTAACTGGTCGTCTAATCCTTTTTCAGGTTCAGCCAACCTTAGCAGTGCAGGATTTCTGGACTCATCTGGAAAACCAGATTGTAGCAAGGAACTTAGGTCAAGAAAGAGGGAGCATCCTGGATCATGCTCTGCTTCTGATACCAAAGCCTGCAG...

CDS

Download CDS FASTA

726 bp · LXL04_010109|LXL04_010109|OH1004|CDS

ATGGTTGCCCCTGAAGACGATGATAATTCCAATTGTTTCCTCGATTATAGCTTAATCGAGCAGATTCCAGTCCCCGGAGGCGAACTTCCGTATCTTGAATCGGATTTTAACTGGTCGTCTAATCCTTTTTCAGGTTCAGCCAACCTTAGCAGTGCAGGATTTCTGGACTCATCTGGAAAACCAGATTGTAGCAAGGAACTTAGGTCAAGAAAGAGGGAGCATCCTGGATCATGCTCTGCTTCTGATACCAAAGCCTGCAG...

Protein

Download Protein FASTA

241 aa · LXL04_010109|LXL04_010109|OH1004|PROTEIN

MVAPEDDDNSNCFLDYSLIEQIPVPGGELPYLESDFNWSSNPFSGSANLSSAGFLDSSGKPDCSKELRSRKREHPGSCSASDTKACREKRRRDKLNERFQELNEILDPGRPPKTDKTVILSDAIRKVTHLREEAMKLKDSAKDLQAKINELKVEKNELRDEKQKMKAEKERLEQQVKALSSAPAPAAFFPPPPPHSGMTMAFPANGKFMPVMGYHGVPMWPFASTAAVDTSEDHVHRSRAA

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_010109`
TK1151 ID	TkA03G498930
OH-1004 ID	LXL04_010109
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.200
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_010109

Location Chr02:140311649-140313031 (-)

Description Similar to ILR3: Transcription factor ILR3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g54680`	Transcription factor.	An Arabidopsis basic helix-loop-helix leucine zipper protein modulates metal homeostasis and auxin conjugate responsiveness.2006 · DOI: 10.1534/genetics.106.061044
`At1g51070`	Transcription factor bHLH115.	No verified direct reference in this release
`At4g14410`	Transcription factor bHLH104.	No verified direct reference in this release
`At3g23210`	Transcription factor bHLH34.	No verified direct reference in this release
`At3g19860`	Transcription factor bHLH121.	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_010109 · 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:0006879 intracellular iron ion homeostasis Biological Process

GO:0010030 positive regulation of seed germination Biological Process

GO:0019760 glucosinolate metabolic process Biological Process

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

GO:0071333 cellular response to glucose stimulus Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0043565 sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G51070

ath:AT3G19860

ath:AT3G23210

ath:AT4G14410

ath:AT5G54680

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.

Nucleus0.971

Rank 1 · LXL04_010109 · OH-1004

Cytoplasm0.121

Rank 2 · LXL04_010109 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_010109 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_010109 · OH-1004

Mitochondrion0.008

Rank 5 · LXL04_010109 · 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.

PF23177.2bHLH_IRO380-169 aa

PF00010.32HLH83-130 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010109	`PF23177.2`	bHLH_IRO3	80	169	6.4e-37	126.5
LXL04_010109	`PF00010.32`	HLH	83	130	7.3e-10	39.2

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
`Q9FH37`	Arabidopsis thaliana	Transcription factor ILR3	50.820%	Swiss-Prot	strong database homology
`Q9C682`	Arabidopsis thaliana	Transcription factor bHLH115	48.954%	Swiss-Prot	moderate database homology
`Q8L467`	Arabidopsis thaliana	Transcription factor bHLH104	48.571%	Swiss-Prot	moderate database homology
`Q9LTC7`	Arabidopsis thaliana	Transcription factor bHLH34	45.455%	Swiss-Prot	moderate database homology
`Q9LT23`	Arabidopsis thaliana	Transcription factor bHLH121	44.554%	Swiss-Prot	weak database homology

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