LXL04_024040 | RubberDandelionOmics

Gene overview

LXL04_024040

Reference: OH-1004 Chr: Chr05 Coordinates: 78439378-78441409 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1089 bp · LXL04_024040|LXL04_024040|OH1004|cDNA

ATGAAGAGATCATGCAATATGTTCATTAGGGAGCCAAATCTACATGCTTTTGTTGCCTTGGCACTTGTTAAATGTAAGCCTCTCACATCCTCCATTATATGCATTCAAATTGCATCACAATTCACCTTACAATTTACTCTTTTCGTTAGTAAAATTTTGATGGGAAGACGACCTCCTTGTTGCGATAAATCGCATGTTAAGAAAGGGCCATGGACTGCTGAAGAAGATGCCAAGATTCTTGCCTATGTTGCTAGTCATGG...

CDS

Download CDS FASTA

1089 bp · LXL04_024040|LXL04_024040|OH1004|CDS

ATGAAGAGATCATGCAATATGTTCATTAGGGAGCCAAATCTACATGCTTTTGTTGCCTTGGCACTTGTTAAATGTAAGCCTCTCACATCCTCCATTATATGCATTCAAATTGCATCACAATTCACCTTACAATTTACTCTTTTCGTTAGTAAAATTTTGATGGGAAGACGACCTCCTTGTTGCGATAAATCGCATGTTAAGAAAGGGCCATGGACTGCTGAAGAAGATGCCAAGATTCTTGCCTATGTTGCTAGTCATGG...

Protein

Download Protein FASTA

362 aa · LXL04_024040|LXL04_024040|OH1004|PROTEIN

MKRSCNMFIREPNLHAFVALALVKCKPLTSSIICIQIASQFTLQFTLFVSKILMGRRPPCCDKSHVKKGPWTAEEDAKILAYVASHGIGNWTLVPQKAGLNRCGKSCRLRWTNYLRPDLKHDSFTPHEEQLILRYHQAIGSRWSLIAKQLPGRTDNDVKNHWNTKLKKKLSKMGIDPITHKPFGQLLSDYGNINEIVPTATQNTNHRHPEPPDFSLADSSLTIIDPFQDQQHHHQINNLLTPPHFHINEAASSSTSSPAS...

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_024040`
TK1151 ID	TkA06G185530
OH-1004 ID	LXL04_024040
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.100
Protein coverage (%)	TK1151 100.000 / OH-1004 85.359 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_024040

Location Chr05:78439378-78441409 (-)

Description Similar to MYB35: Transcription factor MYB35

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g28470`	Required for anther development and early tapetal function during microspore maturation.	Defective in Tapetal development and function 1 is essential for anther development and tapetal function for microspore maturation in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03500.x A genetic pathway for tapetum development and function in Arabidopsis.2011 · DOI: 10.1111/j.1744-7909.2011.01078.x
`At5g56110`	Transcription factor that binds to the DNA sequence 5'- CCAACC-3'.	AtMYB103 regulates tapetum and trichome development in Arabidopsis thaliana.2003 · DOI: 10.1046/j.1365-313x.2003.01791.x Transcription factor AtMYB103 is required for anther development by regulating tapetum development, callose dissolution and exine formation in Arabidopsis.2007 · DOI: 10.1111/j.1365-313x.2007.03254.x The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana.2011 · DOI: 10.1105/tpc.110.082651
`At3g01140`	Functions as a repressor of epidermal cell outgrowth and negatively regulate trichome branch formation.	Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106.2008 · DOI: 10.1104/pp.108.126979 MIXTA-like transcription factors and WAX INDUCER1/SHINE1 coordinately regulate cuticle development in Arabidopsis and Torenia fournieri.2013 · DOI: 10.1105/tpc.113.110783 The MIXTA-like transcription factor MYB16 is a major regulator of cuticle formation in vegetative organs.2013 · DOI: 10.4161/psb.26826
`At5g15310`	Involved in the control of epidermal cell morphogenesis in petals.	Control of cell and petal morphogenesis by R2R3 MYB transcription factors.2007 · DOI: 10.1242/dev.02836 MIXTA-like transcription factors and WAX INDUCER1/SHINE1 coordinately regulate cuticle development in Arabidopsis and Torenia fournieri.2013 · DOI: 10.1105/tpc.113.110783 The MIXTA-like transcription factor MYB16 is a major regulator of cuticle formation in vegetative organs.2013 · DOI: 10.4161/psb.26826

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0470600`	Essential for tapetum development in anthers and microsporogenesis.	MYB80, a regulator of tapetal and pollen development, is functionally conserved in crops.2012 · DOI: 10.1007/s11103-011-9855-0

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024040 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000902 cell morphogenesis Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009555 pollen development Biological Process

GO:0010090 trichome morphogenesis Biological Process

GO:0010091 trichome branching Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0052545 callose localization Biological Process

GO:0055046 microgametogenesis Biological Process

GO:1901957 regulation of cutin biosynthetic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G01140

ath:AT3G28470

ath:AT5G15310

ath:AT5G56110

osa:9272494

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.

Nucleus0.846

Rank 1 · LXL04_024040 · OH-1004

Cytoplasm0.259

Rank 2 · LXL04_024040 · OH-1004

Mitochondrion0.028

Rank 3 · LXL04_024040 · OH-1004

Cell membrane0.022

Rank 4 · LXL04_024040 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_024040 · 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-binding68-115 aa

PF13921.13Myb_DNA-bind_671-130 aa

PF00249.38Myb_DNA-binding122-164 aa

PF13921.13Myb_DNA-bind_6124-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024040	`PF00249.38`	Myb_DNA-binding	68	115	1.1e-35	122.1
LXL04_024040	`PF13921.13`	Myb_DNA-bind_6	71	130	4e-21	75.7
LXL04_024040	`PF00249.38`	Myb_DNA-binding	122	164	1.1e-35	122.1
LXL04_024040	`PF13921.13`	Myb_DNA-bind_6	124	172	4e-21	75.7

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
`Q9LSI7`	Arabidopsis thaliana	Transcription factor MYB35	45.619%	Swiss-Prot	moderate database homology
`Q9XHV0`	Arabidopsis thaliana	Transcription factor MYB80	54.639%	Swiss-Prot	moderate database homology
`Q9LE63`	Arabidopsis thaliana	Transcription factor MYB106	64.444%	Swiss-Prot	weak database homology
`Q9LXF1`	Arabidopsis thaliana	Transcription factor MYB16	38.658%	Swiss-Prot	moderate database homology
`Q7XQN1`	Oryza sativa subsp. japonica	Transcription factor MYB80	67.669%	Swiss-Prot	weak database homology

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