LXL04_000620 | RubberDandelionOmics

Gene overview

LXL04_000620

Reference: OH-1004 Chr: Chr01 Coordinates: 11241917-11243553 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1203 bp · LXL04_000620|LXL04_000620|OH1004|cDNA

ATGGAAGGTGGTGGTCACAGTGGCTATGGCGGTTCCCGTGGTGATTATGGTGGTGGATTTGCTAATCACGCGAATTATCAAAACCATCTTTCCTGGTATCGGCCTGCACCTCCACCATTGACAGCCATAGATAGATTCTTATGGGGCCATACTCCAACTCCAATCGATCAAACTCAAAACCATGAAATCAGCGAAGCATTCATCCCCTCAAATGGCGGCATCATCGACCAAAGTGGATTAATACGTTTTGCACCATGTTC...

CDS

Download CDS FASTA

1203 bp · LXL04_000620|LXL04_000620|OH1004|CDS

ATGGAAGGTGGTGGTCACAGTGGCTATGGCGGTTCCCGTGGTGATTATGGTGGTGGATTTGCTAATCACGCGAATTATCAAAACCATCTTTCCTGGTATCGGCCTGCACCTCCACCATTGACAGCCATAGATAGATTCTTATGGGGCCATACTCCAACTCCAATCGATCAAACTCAAAACCATGAAATCAGCGAAGCATTCATCCCCTCAAATGGCGGCATCATCGACCAAAGTGGATTAATACGTTTTGCACCATGTTC...

Protein

Download Protein FASTA

400 aa · LXL04_000620|LXL04_000620|OH1004|PROTEIN

MEGGGHSGYGGSRGDYGGGFANHANYQNHLSWYRPAPPPLTAIDRFLWGHTPTPIDQTQNHEISEAFIPSNGGIIDQSGLIRFAPCSPIMVTNDVFFNDIGECLTWEELKNYPNYDPNHGLINQVEVIKSVKISRGSTKQSKGGNNSKLLIKGQWTEEEDSKLIRLVKQHGITKWAVIAEKMTGRAGKQCRERWRNHLRPDIRKDTWSEEEVRMLIDAHQKVGNKWAEIAKLIPGRTENAIKNQWNATKRRQNSSRKSKK...

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_000620`
TK1151 ID	TkA01G598960
OH-1004 ID	LXL04_000620
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	70.100
Protein coverage (%)	TK1151 100.000 / OH-1004 77.750 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_000620

Location Chr01:11241917-11243553 (-)

Description Similar to MYB119: Transcription factor MYB119

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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_000620 · 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.

Nucleus0.909

Rank 1 · LXL04_000620 · OH-1004

Cytoplasm0.187

Rank 2 · LXL04_000620 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_000620 · OH-1004

Mitochondrion0.016

Rank 4 · LXL04_000620 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_000620 · 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-binding152-198 aa

PF13921.13Myb_DNA-bind_6155-215 aa

PF15963.12Myb_DNA-bind_7203-261 aa

PF00249.38Myb_DNA-binding204-246 aa

PF13921.13Myb_DNA-bind_6207-250 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000620	`PF00249.38`	Myb_DNA-binding	152	198	4.4e-34	117.1
LXL04_000620	`PF13921.13`	Myb_DNA-bind_6	155	215	2.9e-26	92.1
LXL04_000620	`PF15963.12`	Myb_DNA-bind_7	203	261	2.7e-06	27.8
LXL04_000620	`PF00249.38`	Myb_DNA-binding	204	246	4.4e-34	117.1
LXL04_000620	`PF13921.13`	Myb_DNA-bind_6	207	250	2.9e-26	92.1

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
`Q9FIM4`	Arabidopsis thaliana	Transcription factor MYB119	42.236%	Swiss-Prot	moderate database homology
`Q9FY60`	Arabidopsis thaliana	Transcription factor MYB64	40.741%	Swiss-Prot	moderate database homology
`Q9S7L2`	Arabidopsis thaliana	Transcription factor MYB98	62.143%	Swiss-Prot	weak database homology
`Q9LVW4`	Arabidopsis thaliana	Transcription factor MYB118	60.294%	Swiss-Prot	weak database homology
`Q1PDP9`	Arabidopsis thaliana	Transcription factor MYB115	44.262%	Swiss-Prot	weak database homology

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