LXL04_006300 | RubberDandelionOmics

Gene overview

LXL04_006300

Reference: OH-1004 Chr: Chr02 Coordinates: 6381307-6382954 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

786 bp · LXL04_006300|LXL04_006300|OH1004|cDNA

acacaccaCACCATGGAACCGTCTTTTGCTCCAAGTAGTATTCTTGATAAAATGACGAAGAGTGCAGAAAAACCAAATGGTAAAGATGAAGTCGACGGTGGTTCACGGCGGAGGTTCGTCGTTAAAGGCCATTGGAAGCCGTCGGAGGACGTTAAGTTACGAGAACTCGTCGCTCTTCATGGGCCGAAAAACTGGAATATGATATCGGAACAACTTCCAGGAAGAACCGGGAAAAGTTGCAGGCTCCGATGGGTGAATCA...

CDS

Download CDS FASTA

774 bp · LXL04_006300|LXL04_006300|OH1004|CDS

ATGGAACCGTCTTTTGCTCCAAGTAGTATTCTTGATAAAATGACGAAGAGTGCAGAAAAACCAAATGGTAAAGATGAAGTCGACGGTGGTTCACGGCGGAGGTTCGTCGTTAAAGGCCATTGGAAGCCGTCGGAGGACGTTAAGTTACGAGAACTCGTCGCTCTTCATGGGCCGAAAAACTGGAATATGATATCGGAACAACTTCCAGGAAGAACCGGGAAAAGTTGCAGGCTCCGATGGGTGAATCAGTTGGACCCACA...

Protein

Download Protein FASTA

257 aa · LXL04_006300|LXL04_006300|OH1004|PROTEIN

MEPSFAPSSILDKMTKSAEKPNGKDEVDGGSRRRFVVKGHWKPSEDVKLRELVALHGPKNWNMISEQLPGRTGKSCRLRWVNQLDPQISTAVFSREEDETLMAAHMVFGNQWSHIAKFFPGRTDNGIKNHWHVLTARRRKHVAGVSNSCSSGSFHRLSGDSGNGSSGSTITLLGKSTLINEGTSLLCMHTPDSVFSGEETKMSLAVADGGDGGGYGGYCNKAMETYGDYNIANPHLTFTSTTISRPLRFIDFLGIGN

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_006300`
TK1151 ID	TkA03G026070
OH-1004 ID	LXL04_006300
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 96.500 / OH-1004 75.097 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_006300

Location Chr02:6381307-6382954 (+)

Description Similar to CSA: Transcription factor CSA

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g69560`	Probable transcription factor that involved in boundary specification, meristem initiation and maintenance, and organ patterning.	LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis.2009 · DOI: 10.1242/dev.031971
`At1g26780`	Probable transcription factor that involved in boundary specification, meristem initiation and maintenance, and organ patterning.	LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis.2009 · DOI: 10.1242/dev.031971 Characterization of constricted fruit (ctf) mutant uncovers a role for AtMYB117/LOF1 in ovule and fruit development in Arabidopsis thaliana.2011 · DOI: 10.1371/journal.pone.0018760
`At5g17800`	Acts as a cell-specific local repressor of quiescent center (QC) self-renewal by cell divisions in the primary root.	MYB56 encoding a R2R3 MYB transcription factor regulates seed size in Arabidopsis thaliana.2013 · DOI: 10.1111/jipb.12094 Regulation of plant stem cell quiescence by a brassinosteroid signaling module.2014 · DOI: 10.1016/j.devcel.2014.05.020 Identification of Arabidopsis MYB56 as a novel substrate for CRL3BPM E3 ligases.2014 · DOI: 10.1093/mp/ssu120
`At1g17950`	Transcription factor that confers sensitivity to abscisic acid (ABA) and salt, but tolerance to drought.	A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.2008 · DOI: 10.1105/tpc.108.061325 Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis.2013 · DOI: 10.3389/fpls.2013.00189

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0274800`	Transcription factor required for sugar partitioning from leaves to anthers during male reproductive development.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006300 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001935 endothelial cell proliferation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0009834 plant-type secondary cell wall biogenesis Biological Process

GO:0010199 organ boundary specification between lateral organs and the meristem Biological Process

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

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

GO:0051782 negative regulation of cell division Biological Process

GO:0071367 cellular response to brassinosteroid stimulus Biological Process

KEGG gene cross-reference

ath:AT1G17950

ath:AT1G26780

ath:AT1G69560

ath:AT5G17800

dosa:Os01g0274800

osa:4325181

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_006300 · OH-1004

Cytoplasm0.080

Rank 2 · LXL04_006300 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_006300 · OH-1004

Plastid0.012

Rank 4 · LXL04_006300 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_006300 · 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.

PF00249.38Myb_DNA-binding38-84 aa

PF13921.13Myb_DNA-bind_641-101 aa

PF00249.38Myb_DNA-binding93-132 aa

PF13921.13Myb_DNA-bind_693-140 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006300	`PF00249.38`	Myb_DNA-binding	38	84	1e-32	112.7
LXL04_006300	`PF13921.13`	Myb_DNA-bind_6	41	101	4e-25	88.5
LXL04_006300	`PF00249.38`	Myb_DNA-binding	93	132	1e-32	112.7
LXL04_006300	`PF13921.13`	Myb_DNA-bind_6	93	140	4e-25	88.5

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
`Q9SEZ4`	Arabidopsis thaliana	Transcription factor MYB105	38.961%	Swiss-Prot	moderate database homology
`Q9LQX5`	Arabidopsis thaliana	Transcription factor MYB117	62.857%	Swiss-Prot	weak database homology
`Q6R053`	Arabidopsis thaliana	Transcription factor MYB56	37.200%	Swiss-Prot	moderate database homology
`Q6R0C4`	Arabidopsis thaliana	Transcription factor MYB52	64.356%	Swiss-Prot	weak database homology
`Q5NBM8`	Oryza sativa subsp. japonica	Transcription factor CSA	59.821%	Swiss-Prot	weak database homology

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