LXL04_016363 | RubberDandelionOmics

Gene overview

LXL04_016363

Reference: OH-1004 Chr: Chr03 Coordinates: 120357258-120358317 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

765 bp · LXL04_016363|LXL04_016363|OH1004|cDNA

AtgggaggaggaggaggaggaggagggcGGTCCCCGTGCTGTGACAAGAATAAGGTGAAGAAAGGGCCGTGGAGTCCGGTGGAGGACGTTAGGCTCGTCTCCTTCATTCAGAAACATGGTCATTCTAATTGGCGTTCTCTCCCTAAAGAAGCTGGTTTGCTAAGGTGTGGAAAGAGCTGCCGCCTGAGGTGGATAAATTATCTAAGGCCTGACCTCAAAAGAGGCAATTTTACTCCCCTAGAAGAGCATTCCATAATTCG...

CDS

Download CDS FASTA

765 bp · LXL04_016363|LXL04_016363|OH1004|CDS

ATGGGAGGAGGAGGAGGAGGAGGAGGGCGGTCCCCGTGCTGTGACAAGAATAAGGTGAAGAAAGGGCCGTGGAGTCCGGTGGAGGACGTTAGGCTCGTCTCCTTCATTCAGAAACATGGTCATTCTAATTGGCGTTCTCTCCCTAAAGAAGCTGGTTTGCTAAGGTGTGGAAAGAGCTGCCGCCTGAGGTGGATAAATTATCTAAGGCCTGACCTCAAAAGAGGCAATTTTACTCCCCTAGAAGAGCATTCCATAATTCG...

Protein

Download Protein FASTA

254 aa · LXL04_016363|LXL04_016363|OH1004|PROTEIN

MGGGGGGGGRSPCCDKNKVKKGPWSPVEDVRLVSFIQKHGHSNWRSLPKEAGLLRCGKSCRLRWINYLRPDLKRGNFTPLEEHSIIRLHATFGNKWSKIASKLPGRTDNEIKNVWNTHLRKRSILMNKNESFLGTNQPHKGIDGEETAGDTLVDHPSTSSSTVSCNTHDEVDLEIPEFELWNMLADIELPYSKPIADHDPNGSMDIDHRVRLLEEELGLVDATPAVVDDNSEMWCKISDDISPLWSPSPQNFGF

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_016363`
TK1151 ID	TkA02G150360
OH-1004 ID	LXL04_016363
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.600
Protein coverage (%)	TK1151 91.633 / OH-1004 90.157 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_016363

Location Chr03:120357258-120358317 (+)

Description Similar to MYB63: Transcription factor MYB63

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g79180`	Transcriptional activator that binds DNA to the AC cis-elements 5'-ACCTACC-3', 5'-ACCAACC-3' and 5'-ACCTAAC-3' of promoters and specifically activates lignin biosynthetic genes during secondary wall formation mediated by SND1.	MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis.2009 · DOI: 10.1105/tpc.108.063321
`At1g16490`	Transcriptional activator that binds DNA to the AC cis-elements 5'-ACCTACC-3', 5'-ACCAACC-3' and 5'-ACCTAAC-3' of promoters and specifically activates lignin biosynthetic genes during secondary wall formation mediated by SND1.	MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis.2009 · DOI: 10.1105/tpc.108.063321
`At1g56160`	Involved in metal ions homeostasis, including iron ions (Fe) acquisition, via the regulation of NAS4 and NAS2 genes expression.	Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd-hyperaccumulator Thlaspi caerulescens.2008 · DOI: 10.1111/j.1365-3040.2007.01764.x MYB72 is required in early signaling steps of rhizobacteria-induced systemic resistance in Arabidopsis.2008 · DOI: 10.1104/pp.107.113829 MYB72, a node of convergence in induced systemic resistance triggered by a fungal and a bacterial beneficial microbe.2009 · DOI: 10.1111/j.1438-8677.2008.00162.x β-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots.2014 · DOI: 10.1111/nph.12980
`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

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016363 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002237 response to molecule of bacterial origin Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009411 response to UV Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009809 lignin biosynthetic process Biological Process

GO:0009866 induced systemic resistance, ethylene mediated signaling pathway Biological Process

GO:0010043 response to zinc ion Biological Process

GO:0010447 response to acidic pH Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0019748 secondary metabolic process Biological Process

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

KEGG gene cross-reference

ath:AT1G16490

ath:AT1G56160

ath:AT1G79180

ath:AT2G31180

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.

Nucleus0.967

Rank 1 · LXL04_016363 · OH-1004

Cytoplasm0.094

Rank 2 · LXL04_016363 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_016363 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_016363 · OH-1004

Plastid0.012

Rank 5 · LXL04_016363 · 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-binding21-68 aa

PF13921.13Myb_DNA-bind_624-83 aa

PF00249.38Myb_DNA-binding74-119 aa

PF13921.13Myb_DNA-bind_677-121 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016363	`PF00249.38`	Myb_DNA-binding	21	68	2.7e-34	117.7
LXL04_016363	`PF13921.13`	Myb_DNA-bind_6	24	83	1e-18	67.9
LXL04_016363	`PF00249.38`	Myb_DNA-binding	74	119	2.7e-34	117.7
LXL04_016363	`PF13921.13`	Myb_DNA-bind_6	77	121	1e-18	67.9

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
`Q6R0A6`	Arabidopsis thaliana	Transcription factor MYB63	80.172%	Swiss-Prot	weak database homology
`Q9SA47`	Arabidopsis thaliana	Transcription factor MYB58	79.310%	Swiss-Prot	weak database homology
`Q9SGU3`	Arabidopsis thaliana	Transcription factor MYB72	81.034%	Swiss-Prot	weak database homology
`Q9SJX8`	Arabidopsis thaliana	Transcription factor MYB14	59.509%	Swiss-Prot	moderate database homology

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