LXL04_021397 | RubberDandelionOmics

Gene overview

LXL04_021397

Reference: OH-1004 Chr: Chr04 Coordinates: 128728879-128730410 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1086 bp · LXL04_021397|LXL04_021397|OH1004|cDNA

ATGGTTACTTACAATAATCCAAGTGATTACACAGAAAAAATGGAGAAATGTCGAGAATATATGGAAGCTTTAGAAGAAGAACGTAGAAAGATTCGAGTATTCGAACGTGAGCTTCCTCTTTGTCATGAACTTGTCTCTCAAGCGATTGAAAGATGcagagagcaaatgtcggggAAGATGATGGATTGCTTTAATGGTGAATTTGATCAGTATTCTGAGCAAACATCCAGTGAGGGTCCCGTTTTGGAAGAGTTTATTCC...

CDS

Download CDS FASTA

1086 bp · LXL04_021397|LXL04_021397|OH1004|CDS

ATGGTTACTTACAATAATCCAAGTGATTACACAGAAAAAATGGAGAAATGTCGAGAATATATGGAAGCTTTAGAAGAAGAACGTAGAAAGATTCGAGTATTCGAACGTGAGCTTCCTCTTTGTCATGAACTTGTCTCTCAAGCGATTGAAAGATGCAGAGAGCAAATGTCGGGGAAGATGATGGATTGCTTTAATGGTGAATTTGATCAGTATTCTGAGCAAACATCCAGTGAGGGTCCCGTTTTGGAAGAGTTTATTCC...

Protein

Download Protein FASTA

361 aa · LXL04_021397|LXL04_021397|OH1004|PROTEIN

MVTYNNPSDYTEKMEKCREYMEALEEERRKIRVFERELPLCHELVSQAIERCREQMSGKMMDCFNGEFDQYSEQTSSEGPVLEEFIPIKRASSTNDDDVDYGQQKQQLSHNSKIIYSIDKSSQISTKSDWLTSTQLSIKTPDPHIEQDLLSNKLVAMETSRNGYGAFHPFTKPAVVANAANSCSAETDGGGGSGSKGEDKGLYNKKERRCWSPELHRRFLHALQQLGGAHIATPKQIKELMKVDGLTNDEIKSHLQKYRL...

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_021397`
TK1151 ID	TkA05G386440
OH-1004 ID	LXL04_021397
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_021397

Location Chr04:128728879-128730410 (-)

Description Similar to HHO3: Transcription factor HHO3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g25550`	Probable transcription factor involved in phosphate signaling in roots.	No verified direct reference in this release
`At1g68670`	Probable transcription factor involved in phosphate homeostasis.	Arabidopsis MYB-Related HHO2 Exerts a Regulatory Influence on a Subset of Root Traits and Genes Governing Phosphate Homeostasis.2016 · DOI: 10.1093/pcp/pcw063
`At1g13300`	Transcription factor involved in nitrate and phosphate signaling in roots.	Overexpressing HRS1 confers hypersensitivity to low phosphate-elicited inhibition of primary root growth in Arabidopsis thaliana.2009 · DOI: 10.1111/j.1744-7909.2009.00819.x HRS1 acts as a negative regulator of abscisic acid signaling to promote timely germination of Arabidopsis seeds.2012 · DOI: 10.1371/journal.pone.0035764 AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip.2015 · DOI: 10.1038/ncomms7274
`At3g25790`	Probable factor involved in nitrate and phosphate signaling in roots.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0325600`	Transcriptional repressor that may play a role in response to nitrogen.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021397 · 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:0009737 response to abscisic acid Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0016036 cellular response to phosphate starvation Biological Process

GO:0032107 regulation of response to nutrient levels Biological Process

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

GO:0055062 phosphate ion homeostasis Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0080022 primary root development Biological Process

GO:0090548 response to nitrate starvation Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G13300

ath:AT1G25550

ath:AT1G68670

ath:AT3G25790

dosa:Os02g0325600

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.

Nucleus0.966

Rank 1 · LXL04_021397 · OH-1004

Cytoplasm0.104

Rank 2 · LXL04_021397 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_021397 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_021397 · OH-1004

Plastid0.010

Rank 5 · LXL04_021397 · 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.

PF26575.1HHO5_N9-56 aa

PF00249.38Myb_DNA-binding208-259 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021397	`PF26575.1`	HHO5_N	9	56	6.7e-15	55.6
LXL04_021397	`PF00249.38`	Myb_DNA-binding	208	259	1.1e-07	32.6

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
`Q9FPE8`	Arabidopsis thaliana	Transcription factor HHO3	44.412%	Swiss-Prot	moderate database homology
`Q8VZS3`	Arabidopsis thaliana	Transcription factor HHO2	43.881%	Swiss-Prot	moderate database homology
`Q9FX67`	Arabidopsis thaliana	Transcription factor HRS1	46.367%	Swiss-Prot	moderate database homology
`Q9LS00`	Arabidopsis thaliana	Transcription factor HHO1	43.077%	Swiss-Prot	moderate database homology
`Q6Z869`	Oryza sativa subsp. japonica	Transcription factor NIGT1	41.047%	Swiss-Prot	moderate database homology

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