LXL04_028018 | RubberDandelionOmics

Gene overview

LXL04_028018

Reference: OH-1004 Chr: Chr06 Coordinates: 28930515-28933923 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1614 bp · LXL04_028018|LXL04_028018|OH1004|cDNA

ATGGCCTCGGCGTCAGAGTTAAGTCTTGAATGCAAACCCCACAGCTACTCCATGGCCTTGAAAACGATTGGAGAACAACAACTAAATAACACAAATGATCAAACGCAAAAACTCGAAGAGTTTCTTTCTCGTCTTGAAGAAGAACGACTCAAGATCGATGCTTTTAAGCGTGAACTTCCTCTTTGCATGCAACTCCTCACCAATGCCATGGAGACATCAAGACAACAATTACAAACATACCGTGCTAATCAAGGCTCACC...

CDS

Download CDS FASTA

1614 bp · LXL04_028018|LXL04_028018|OH1004|CDS

ATGGCCTCGGCGTCAGAGTTAAGTCTTGAATGCAAACCCCACAGCTACTCCATGGCCTTGAAAACGATTGGAGAACAACAACTAAATAACACAAATGATCAAACGCAAAAACTCGAAGAGTTTCTTTCTCGTCTTGAAGAAGAACGACTCAAGATCGATGCTTTTAAGCGTGAACTTCCTCTTTGCATGCAACTCCTCACCAATGCCATGGAGACATCAAGACAACAATTACAAACATACCGTGCTAATCAAGGCTCACC...

Protein

Download Protein FASTA

537 aa · LXL04_028018|LXL04_028018|OH1004|PROTEIN

MASASELSLECKPHSYSMALKTIGEQQLNNTNDQTQKLEEFLSRLEEERLKIDAFKRELPLCMQLLTNAMETSRQQLQTYRANQGSPVLEEFIPLKNLNTEGPEKVSLSSIDNKANWMTSAQLWSQASSTITTAMDNNNNHLKTAQNSTQTDIDFNTKQRNGGAFIPFSKEGNSSCATPGLVLPELALSSGDKDVDHEDNKSCLRENNTSIKGGNINGDVSDTQTTTTATGSGANSSQTHRKTRRCWSPDLHRRFVNALQ...

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_028018`
TK1151 ID	TkA07G113370
OH-1004 ID	LXL04_028018
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.500
Protein coverage (%)	TK1151 78.205 / OH-1004 98.138 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_028018

Location Chr06:28930515-28933923 (+)

Description Similar to EFM: Myb family transcription factor EFM

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g03500`	Transcription factor acting as a flowering repressor, directly repressing FT expression in a dosage-dependent manner in the leaf vasculature.	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
`At1g25550`	Probable transcription factor involved in phosphate signaling in roots.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0176700`	Probable transcription factor that may play a role in regulatory networks controlling development and metabolism.	No verified direct reference in this release
`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_028018 · 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:0009266 response to temperature stimulus Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0016036 cellular response to phosphate starvation Biological Process

GO:0034244 negative regulation of transcription elongation by RNA polymerase II Biological Process

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

GO:0048579 negative regulation of long-day photoperiodism, flowering Biological Process

GO:0055062 phosphate ion homeostasis Biological Process

GO:0071456 cellular response to hypoxia Biological Process

KEGG gene cross-reference

ath:AT1G25550

ath:AT1G68670

ath:AT2G03500

dosa:Os01g0176700

dosa:Os02g0325600

osa:4326224

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.

Nucleus0.947

Rank 1 · LXL04_028018 · OH-1004

Cytoplasm0.119

Rank 2 · LXL04_028018 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_028018 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_028018 · OH-1004

Mitochondrion0.012

Rank 5 · LXL04_028018 · 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_N11-78 aa

PF00249.38Myb_DNA-binding244-295 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028018	`PF26575.1`	HHO5_N	11	78	1.8e-27	95.9
LXL04_028018	`PF00249.38`	Myb_DNA-binding	244	295	7.4e-07	29.9

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
`Q9ZQ85`	Arabidopsis thaliana	Myb family transcription factor EFM	55.348%	Swiss-Prot	moderate database homology
`Q8VZS3`	Arabidopsis thaliana	Transcription factor HHO2	40.557%	Swiss-Prot	moderate database homology
`Q9FPE8`	Arabidopsis thaliana	Transcription factor HHO3	37.117%	Swiss-Prot	moderate database homology
`Q5VRW2`	Oryza sativa subsp. japonica	Transcription factor NIGTH1	47.568%	Swiss-Prot	moderate database homology
`Q6Z869`	Oryza sativa subsp. japonica	Transcription factor NIGT1	38.393%	Swiss-Prot	moderate database homology

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