LXL04_006124 | RubberDandelionOmics

Gene overview

LXL04_006124

Reference: OH-1004 Chr: Chr02 Coordinates: 2033189-2035204 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

825 bp · LXL04_006124|LXL04_006124|OH1004|cDNA

ATGGATCAAGAATCATTTGGTAATCAATTCAATCTTCAAATGTTTGGATACGGAATGGAATTCGTGAATCCTCCGATGGAATTGAAGAAAGGAAATGGTAGGAAGAATAAGGCGAAAAGGAAGAGTAGTAATAAAGGTTGGCGGAAAGCGGTAATCGTTAAAGGACAATGGAATTCCGAAGAAGACAGGTTATTAGTGCAGTTAGTGAAGCAATATGGGGATACCAAATGGTCCAGAATTGCTGAAAAGCTTCCTGGAAG...

CDS

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825 bp · LXL04_006124|LXL04_006124|OH1004|CDS

ATGGATCAAGAATCATTTGGTAATCAATTCAATCTTCAAATGTTTGGATACGGAATGGAATTCGTGAATCCTCCGATGGAATTGAAGAAAGGAAATGGTAGGAAGAATAAGGCGAAAAGGAAGAGTAGTAATAAAGGTTGGCGGAAAGCGGTAATCGTTAAAGGACAATGGAATTCCGAAGAAGACAGGTTATTAGTGCAGTTAGTGAAGCAATATGGGGATACCAAATGGTCCAGAATTGCTGAAAAGCTTCCTGGAAG...

Protein

Download Protein FASTA

274 aa · LXL04_006124|LXL04_006124|OH1004|PROTEIN

MDQESFGNQFNLQMFGYGMEFVNPPMELKKGNGRKNKAKRKSSNKGWRKAVIVKGQWNSEEDRLLVQLVKQYGDTKWSRIAEKLPGRIAKQCRDRWQNHLRPDITKDAWSEEEDKLLIAIHKEVGNKWSEIARRLPGRSENTIKNHWNATKRRQLSSRRRGKPKYMSLLQEYIRSVPSSSSSSSSDDQIINIKVNNNDKRSQVVRPPLDPPVHVNATSSSSFEEYNLDAMHDYVPGWSTVNESIFDFDHVPLHLTSHLEF...

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_006124`
TK1151 ID	TkA03G010550
OH-1004 ID	LXL04_006124
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 98.598 / OH-1004 77.007 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_006124

Location Chr02:2033189-2035204 (-)

Description Similar to MYB98: Transcription factor MYB98

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g18770`	Transcription factor that binds to the motif 5'-GTAACNT-3' in the promoter of target genes (e.g. DD11 and DD18) and promotes their expression within synergid cells (e.g. in the filiform apparatus) in ovules.	MYB98 is required for pollen tube guidance and synergid cell differentiation in Arabidopsis.2005 · DOI: 10.1105/tpc.105.034603 Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins.2007 · DOI: 10.1371/journal.pgen.0030171 Cytoplasmic Ca2+ changes dynamically during the interaction of the pollen tube with synergid cells.2012 · DOI: 10.1242/dev.081208
`At3g27785`	Transcription activator that recognizes the motif 5'-TAACGG-3' in the promoter of endosperm-induced genes.	Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis.2009 · DOI: 10.1038/cr.2008.276 Involvement of an R2R3-MYB transcription factor gene AtMYB118 in embryogenesis in Arabidopsis.2009 · DOI: 10.1007/s00299-008-0644-4 MYB118 represses endosperm maturation in seeds of Arabidopsis.2014 · DOI: 10.1105/tpc.114.130021 Transcriptional Activation of Two Delta-9 Palmitoyl-ACP Desaturase Genes by MYB115 and MYB118 Is Critical for Biosynthesis of Omega-7 Monounsaturated Fatty Acids in the Endosperm of Arabidopsis Seeds.2016 · DOI: 10.1105/tpc.16.00612
`At5g58850`	Transcription factor required for female gametophyte fertility.	MYB64 and MYB119 are required for cellularization and differentiation during female gametogenesis in Arabidopsis thaliana.2013 · DOI: 10.1371/journal.pgen.1003783
`At5g11050`	Transcription factor required for female gametophyte fertility.	MYB64 and MYB119 are required for cellularization and differentiation during female gametogenesis in Arabidopsis thaliana.2013 · DOI: 10.1371/journal.pgen.1003783
`At5g40360`	Transcription activator that recognizes the motif 5'-TAACGG-3' in the promoter of target genes.	Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis.2009 · DOI: 10.1038/cr.2008.276 Transcriptional Activation of Two Delta-9 Palmitoyl-ACP Desaturase Genes by MYB115 and MYB118 Is Critical for Biosynthesis of Omega-7 Monounsaturated Fatty Acids in the Endosperm of Arabidopsis Seeds.2016 · DOI: 10.1105/tpc.16.00612

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006124 · 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:0009553 embryo sac development Biological Process

GO:0009960 endosperm development Biological Process

GO:0010183 pollen tube guidance Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0010262 somatic embryogenesis Biological Process

GO:0010439 regulation of glucosinolate biosynthetic process Biological Process

GO:0045691 regulation of embryo sac central cell differentiation Biological Process

GO:0045697 regulation of synergid differentiation Biological Process

GO:0045723 positive regulation of fatty acid biosynthetic process Biological Process

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

KEGG gene cross-reference

ath:AT3G27785

ath:AT4G18770

ath:AT5G11050

ath:AT5G40360

ath:AT5G58850

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.

Nucleus0.956

Rank 1 · LXL04_006124 · OH-1004

Cytoplasm0.137

Rank 2 · LXL04_006124 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_006124 · OH-1004

Mitochondrion0.012

Rank 4 · LXL04_006124 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_006124 · 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-binding54-100 aa

PF13921.13Myb_DNA-bind_657-114 aa

PF00249.38Myb_DNA-binding106-148 aa

PF13921.13Myb_DNA-bind_6109-151 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006124	`PF00249.38`	Myb_DNA-binding	54	100	1.8e-35	121.5
LXL04_006124	`PF13921.13`	Myb_DNA-bind_6	57	114	1.3e-28	99.6
LXL04_006124	`PF00249.38`	Myb_DNA-binding	106	148	1.8e-35	121.5
LXL04_006124	`PF13921.13`	Myb_DNA-bind_6	109	151	1.3e-28	99.6

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
`Q9S7L2`	Arabidopsis thaliana	Transcription factor MYB98	64.085%	Swiss-Prot	moderate database homology
`Q9LVW4`	Arabidopsis thaliana	Transcription factor MYB118	60.000%	Swiss-Prot	moderate database homology
`Q9FIM4`	Arabidopsis thaliana	Transcription factor MYB119	42.723%	Swiss-Prot	moderate database homology
`Q9FY60`	Arabidopsis thaliana	Transcription factor MYB64	46.286%	Swiss-Prot	moderate database homology
`Q1PDP9`	Arabidopsis thaliana	Transcription factor MYB115	56.818%	Swiss-Prot	weak database homology

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