LXL04_012163 | RubberDandelionOmics

Gene overview

LXL04_012163

Reference: OH-1004 Chr: Chr03 Coordinates: 7575308-7576526 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

624 bp · LXL04_012163|LXL04_012163|OH1004|cDNA

ATGGTGAGGGCACCTTGCATCGACAAAAATGGCATGAAAAAGGGAGCTTGGAGCGAAGAAGAAGATAATAAGCTACGAGATTACATTGAACGGTATGGCCACTGGAATTGGCGTGAACTTCCGAAGTATGCCGGTTTATCAAGGTGCGGCAAGAGTTGCAGATTGAGATGGATGAATTATCTTAGACCAAGCGTGAAACGCGGAAATTTTAGcaaggaagaagaagatatCATCATCAAATTTCATCAAGACATGGGAAA...

CDS

Download CDS FASTA

624 bp · LXL04_012163|LXL04_012163|OH1004|CDS

ATGGTGAGGGCACCTTGCATCGACAAAAATGGCATGAAAAAGGGAGCTTGGAGCGAAGAAGAAGATAATAAGCTACGAGATTACATTGAACGGTATGGCCACTGGAATTGGCGTGAACTTCCGAAGTATGCCGGTTTATCAAGGTGCGGCAAGAGTTGCAGATTGAGATGGATGAATTATCTTAGACCAAGCGTGAAACGCGGAAATTTTAGCAAGGAAGAAGAAGATATCATCATCAAATTTCATCAAGACATGGGAAA...

Protein

Download Protein FASTA

207 aa · LXL04_012163|LXL04_012163|OH1004|PROTEIN

MVRAPCIDKNGMKKGAWSEEEDNKLRDYIERYGHWNWRELPKYAGLSRCGKSCRLRWMNYLRPSVKRGNFSKEEEDIIIKFHQDMGNKWSAIAAQLPGRSDNEIKNHWHTHLKKRSTKHNHQVPHDLKEEQNLNMERIINFAGLPPSVVSTSSDNRISNESTSSHRLSDDSNSMSRPCLQQRLLIDLNQEYVESWEEDSKSEKEFEC

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_012163`
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_012163

Location Chr03:7575308-7576526 (+)

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
`At4g28110`	Transcription factor involved in salt stress response.	AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis.2009 · DOI: 10.1104/pp.108.134874 Phosphorylation by AtMPK6 is required for the biological function of AtMYB41 in Arabidopsis.2012 · DOI: 10.1016/j.bbrc.2012.04.137 AtMYB41 activates ectopic suberin synthesis and assembly in multiple plant species and cell types.2014 · DOI: 10.1111/tpj.12624
`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
`At4g21440`	Probable transcription factor that may function in osmotic stress and wounding signaling pathways (Probable).	Integration of wounding and osmotic stress signals determines the expression of the AtMYB102 transcription factor gene.2003 · DOI: 10.1104/pp.102.019273 The Arabidopsis thaliana Transcription Factor AtMYB102 Functions in Defense Against the Insect Herbivore Pieris rapae.2006 · DOI: 10.4161/psb.1.6.3512
`At2g31180`	Transcription activator that regulates freezing tolerance by affecting expression of CBF genes.	AtMYB14 Regulates Cold Tolerance in Arabidopsis. 2013 · DOI: 10.1007/s11105-012-0481-z

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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012163 · 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:0006952 defense response Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009611 response to wounding Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009825 multidimensional cell growth Biological Process

GO:0010143 cutin biosynthetic process Biological Process

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

KEGG gene cross-reference

ath:AT2G31180

ath:AT3G23250

ath:AT4G21440

ath:AT4G28110

dosa:Os04g0517100

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.

Nucleus0.942

Rank 1 · LXL04_012163 · OH-1004

Cytoplasm0.172

Rank 2 · LXL04_012163 · OH-1004

Mitochondrion0.023

Rank 3 · LXL04_012163 · OH-1004

Cell membrane0.016

Rank 4 · LXL04_012163 · OH-1004

Endoplasmic reticulum0.006

Rank 5 · LXL04_012163 · 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-binding14-61 aa

PF13921.13Myb_DNA-bind_617-75 aa

PF00249.38Myb_DNA-binding67-112 aa

PF13921.13Myb_DNA-bind_670-115 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012163	`PF00249.38`	Myb_DNA-binding	14	61	7.2e-35	119.6
LXL04_012163	`PF13921.13`	Myb_DNA-bind_6	17	75	1e-23	84.0
LXL04_012163	`PF00249.38`	Myb_DNA-binding	67	112	7.2e-35	119.6
LXL04_012163	`PF13921.13`	Myb_DNA-bind_6	70	115	1e-23	84.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9M0J5`	Arabidopsis thaliana	Transcription factor MYB41	71.304%	Swiss-Prot	moderate database homology
`Q9LTC4`	Arabidopsis thaliana	Transcription factor MYB15	70.435%	Swiss-Prot	moderate database homology
`Q9LDR8`	Arabidopsis thaliana	Transcription factor MYB102	67.826%	Swiss-Prot	moderate database homology
`Q9SJX8`	Arabidopsis thaliana	Transcription factor MYB14	48.058%	Swiss-Prot	moderate database homology
`Q7XBH4`	Oryza sativa subsp. japonica	Transcription factor MYB4	72.174%	Swiss-Prot	moderate database homology

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