LXL04_025550 | RubberDandelionOmics

Gene overview

LXL04_025550

Reference: OH-1004 Chr: Chr05 Coordinates: 113376242-113377726 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

735 bp · LXL04_025550|LXL04_025550|OH1004|cDNA

ATGGTAAAGACACCAAGTTTTAACAAAAATGGAGTGATCAAGAAAGGTGCATGGAGTGAAGATGAAGACAATAAGCTAAGAGCATACATCCAAAGATACGGCCATTGGAACTGGCGTTTACTTCCAGAGTTTGCTGGTTTATCTAGAAGTGGGAAGAGTTGCAGGCTTAGATGGATGAATTATCTCCGCCCTAACATAAAACATGGAAACTTTAcaacagaagaagaagatatcATCGTCCAGCTACATAACAAGCTTGG...

CDS

Download CDS FASTA

735 bp · LXL04_025550|LXL04_025550|OH1004|CDS

ATGGTAAAGACACCAAGTTTTAACAAAAATGGAGTGATCAAGAAAGGTGCATGGAGTGAAGATGAAGACAATAAGCTAAGAGCATACATCCAAAGATACGGCCATTGGAACTGGCGTTTACTTCCAGAGTTTGCTGGTTTATCTAGAAGTGGGAAGAGTTGCAGGCTTAGATGGATGAATTATCTCCGCCCTAACATAAAACATGGAAACTTTACAACAGAAGAAGAAGATATCATCGTCCAGCTACATAACAAGCTTGG...

Protein

Download Protein FASTA

244 aa · LXL04_025550|LXL04_025550|OH1004|PROTEIN

MVKTPSFNKNGVIKKGAWSEDEDNKLRAYIQRYGHWNWRLLPEFAGLSRSGKSCRLRWMNYLRPNIKHGNFTTEEEDIIVQLHNKLGNKWSEMAAYLPGRSDNEIKNRWHTHLKKRAQVGQRVLEKEPDNANNKEKFVKISEIKLQQPIESPLSSSSSNLLSYFFNRSNSEGSVEVRPQPVEHTHNFWTEPFLWENDSIISSCDNLFLPTDLDYPAFSKDMIMVDEFLWSSLNSFLQYGDPFIN

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_025550`
TK1151 ID	TkA06G052180
OH-1004 ID	LXL04_025550
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	89.800
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_025550

Location Chr05:113376242-113377726 (-)

Description Similar to MYB4: Transcription factor MYB4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g06180`	Plays a regulatory role in meristem function.	Isolation of Arabidopsis thaliana cDNAs that confer yeast boric acid tolerance.2006 · DOI: 10.1271/bbb.60065 Ectopic expression of a novel MYB gene modifies the architecture of the Arabidopsis inflorescence.1998 · DOI: 10.1046/j.1365-313x.1998.00072.x
`At5g60890`	Transcription factor involved in tryptophan gene activation and in indole-3-acetic acid (IAA) and indolic glucosinolates (IG) biosynthesis.	The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis.2005 · DOI: 10.1104/pp.104.054395 BZR1 and BES1 participate in regulation of glucosinolate biosynthesis by brassinosteroids in Arabidopsis.2013 · DOI: 10.1093/jxb/ert094 A Myb homologue, ATR1, activates tryptophan gene expression in Arabidopsis.1998 · DOI: 10.1073/pnas.95.10.5655
`At3g23250`	Transcription factor involved in cold-regulation of CBF genes and in the development of freezing tolerance.	A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance.2006 · DOI: 10.1074/jbc.m605895200 Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana.2009 · DOI: 10.1016/s1673-8527(09)60003-5

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0517100`	Transcriptional activator involved in cold stress response.	Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants.2004 · DOI: 10.1046/j.1365-313x.2003.01938.x Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development.2010 · DOI: 10.1111/j.1365-3040.2010.02221.x The rice Osmyb4 gene enhances tolerance to frost and improves germination under unfavourable conditions in transgenic barley plants.2012 · DOI: 10.1007/s13353-011-0081-x
`Os02g0624300`	Acts as a negative regulator of cold tolerance.	The OsMYB30 Transcription Factor Suppresses Cold Tolerance by Interacting with a JAZ Protein and Suppressing β-Amylase Expression.2017 · DOI: 10.1104/pp.16.01725

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025550 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000162 L-tryptophan biosynthetic process Biological Process

GO:0002213 defense response to insect Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009759 indole glucosinolate biosynthetic process Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010438 cellular response to sulfur starvation Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

KEGG gene cross-reference

ath:AT1G06180

ath:AT3G23250

ath:AT5G60890

dosa:Os02g0624300

dosa:Os04g0517100

osa:4330027

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.

Nucleus0.877

Rank 1 · LXL04_025550 · OH-1004

Cytoplasm0.253

Rank 2 · LXL04_025550 · OH-1004

Mitochondrion0.027

Rank 3 · LXL04_025550 · OH-1004

Cell membrane0.020

Rank 4 · LXL04_025550 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_025550 · 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.

PF00249.38Myb_DNA-binding15-62 aa

PF13921.13Myb_DNA-bind_618-76 aa

PF00249.38Myb_DNA-binding69-113 aa

PF13921.13Myb_DNA-bind_671-116 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025550	`PF00249.38`	Myb_DNA-binding	15	62	2.4e-33	114.7
LXL04_025550	`PF13921.13`	Myb_DNA-bind_6	18	76	8.8e-23	81.0
LXL04_025550	`PF00249.38`	Myb_DNA-binding	69	113	2.4e-33	114.7
LXL04_025550	`PF13921.13`	Myb_DNA-bind_6	71	116	8.8e-23	81.0

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
`Q9LNC9`	Arabidopsis thaliana	Transcription factor MYB13	56.552%	Swiss-Prot	moderate database homology
`O64399`	Arabidopsis thaliana	Transcription factor MYB34	49.718%	Swiss-Prot	moderate database homology
`Q9LTC4`	Arabidopsis thaliana	Transcription factor MYB15	49.438%	Swiss-Prot	moderate database homology
`Q7XBH4`	Oryza sativa subsp. japonica	Transcription factor MYB4	65.517%	Swiss-Prot	weak database homology
`Q6K1S6`	Oryza sativa subsp. japonica	Transcription factor MYB30	63.559%	Swiss-Prot	weak database homology

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