LXL04_015179 | RubberDandelionOmics

Gene overview

LXL04_015179

Reference: OH-1004 Chr: Chr03 Coordinates: 65372311-65374471 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

387 bp · LXL04_015179|LXL04_015179|OH1004|cDNA

ATGAGAGCTCCGAAATGGGATGCACGATTAGGCTTAAACAGAGGTAAGTGGACTGCCGAAGAAGATGAAAAGTTATTAACCTACATCAGTAAATACGGCATTTGGAATTGGTGTAAGATGCCTCCGTATGCAGGTCTTTCCAGAACCGGAAAAAGTTGCAGGTTAAGATGGATGAATTATTTGAAGCCAAATATAAAACGAGGAAATTTCACAAGTGAAGACGAAGAAACAATAATTCATTACCATTCAATTCTAGGGAA...

CDS

Download CDS FASTA

387 bp · LXL04_015179|LXL04_015179|OH1004|CDS

ATGAGAGCTCCGAAATGGGATGCACGATTAGGCTTAAACAGAGGTAAGTGGACTGCCGAAGAAGATGAAAAGTTATTAACCTACATCAGTAAATACGGCATTTGGAATTGGTGTAAGATGCCTCCGTATGCAGGTCTTTCCAGAACCGGAAAAAGTTGCAGGTTAAGATGGATGAATTATTTGAAGCCAAATATAAAACGAGGAAATTTCACAAGTGAAGACGAAGAAACAATAATTCATTACCATTCAATTCTAGGGAA...

Protein

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128 aa · LXL04_015179|LXL04_015179|OH1004|PROTEIN

MRAPKWDARLGLNRGKWTAEEDEKLLTYISKYGIWNWCKMPPYAGLSRTGKSCRLRWMNYLKPNIKRGNFTSEDEETIIHYHSILGNRWSAIAKKLPGRTDNEVKNYWHAHLMKLGCVLFLGICNAYN

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_015179`
TK1151 ID	TkA02G358380
OH-1004 ID	LXL04_015179
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.100
Protein coverage (%)	TK1151 50.000 / OH-1004 89.062 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_015179

Location Chr03:65372311-65374471 (+)

Description Similar to MYB15: Transcription factor MYB15

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At4g05100`	Probable transcription factor that may function in salt stress response.	Salt-induced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis.2015 · DOI: 10.1093/jxb/erv312
`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
`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
`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_015179 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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:0009737 response to abscisic acid Biological Process

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

GO:0050826 response to freezing Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT2G31180

ath:AT3G23250

ath:AT4G05100

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.

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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.

Nucleus0.818

Rank 1 · LXL04_015179 · OH-1004

Cytoplasm0.197

Rank 2 · LXL04_015179 · OH-1004

Mitochondrion0.045

Rank 3 · LXL04_015179 · OH-1004

Cell membrane0.020

Rank 4 · LXL04_015179 · OH-1004

Plastid0.016

Rank 5 · LXL04_015179 · 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-binding14-61 aa

PF13921.13Myb_DNA-bind_617-76 aa

PF00249.38Myb_DNA-binding67-112 aa

PF13921.13Myb_DNA-bind_670-112 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015179	`PF00249.38`	Myb_DNA-binding	14	61	5.1e-35	120.0
LXL04_015179	`PF13921.13`	Myb_DNA-bind_6	17	76	7.4e-21	74.8
LXL04_015179	`PF00249.38`	Myb_DNA-binding	67	112	5.1e-35	120.0
LXL04_015179	`PF13921.13`	Myb_DNA-bind_6	70	112	7.4e-21	74.8

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
`Q9LTC4`	Arabidopsis thaliana	Transcription factor MYB15	65.487%	Swiss-Prot	strong database homology
`Q9M0Y5`	Arabidopsis thaliana	Transcription factor MYB74	59.016%	Swiss-Prot	strong database homology
`Q9SJX8`	Arabidopsis thaliana	Transcription factor MYB14	63.717%	Swiss-Prot	strong database homology
`Q6K1S6`	Oryza sativa subsp. japonica	Transcription factor MYB30	63.717%	Swiss-Prot	strong database homology
`Q7XBH4`	Oryza sativa subsp. japonica	Transcription factor MYB4	61.947%	Swiss-Prot	strong database homology

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