LXL04_004438 | RubberDandelionOmics

Gene overview

LXL04_004438

Reference: OH-1004 Chr: Chr01 Coordinates: 136182644-136185519 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

966 bp · LXL04_004438|LXL04_004438|OH1004|cDNA

ATGAGGAAGCCGATAGGAGGTCAAGACGATTTGATATTGACGATGAAGATGAGGAAAGGGTTGTGGTCGCCTGAAGAAGATGAAAAGCTAATGAATTACATGATCACAAATGGCCAAGGCTGCTGGAGTGATATCGCACGTAATGCAGGTTTGCAGAGATGCGGTAAAAGCTGTCGGCTCCGTTGGATCAATTACTTGAGGCCTGACCTTAAACGTGGTGCCTTTTCTTCTCAAGAAGAAGAACTCATCGTTCACCTTCA...

CDS

Download CDS FASTA

966 bp · LXL04_004438|LXL04_004438|OH1004|CDS

ATGAGGAAGCCGATAGGAGGTCAAGACGATTTGATATTGACGATGAAGATGAGGAAAGGGTTGTGGTCGCCTGAAGAAGATGAAAAGCTAATGAATTACATGATCACAAATGGCCAAGGCTGCTGGAGTGATATCGCACGTAATGCAGGTTTGCAGAGATGCGGTAAAAGCTGTCGGCTCCGTTGGATCAATTACTTGAGGCCTGACCTTAAACGTGGTGCCTTTTCTTCTCAAGAAGAAGAACTCATCGTTCACCTTCA...

Protein

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321 aa · LXL04_004438|LXL04_004438|OH1004|PROTEIN

MRKPIGGQDDLILTMKMRKGLWSPEEDEKLMNYMITNGQGCWSDIARNAGLQRCGKSCRLRWINYLRPDLKRGAFSSQEEELIVHLHSLLGNRWSQIAARLPGRTDNEIKNFWNSTIKKRLKNSASNSTSLNTSNDSSSSDHQGAMDGFMSIHDSRNIMAMYMDATRQSPSSSSAMQAMTMNHMMEPMPLSDSDDHMHHGRNIAIMDASCYGGNGVSYHGCYEIFGGNLGLADDIFSIPPLENIPNHNQDTKTENPDDRN...

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_004438`
TK1151 ID	TkA01G149140
OH-1004 ID	LXL04_004438
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_004438

Location Chr01:136182644-136185519 (+)

Description Similar to MYB83: Transcription factor MYB83

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g08500`	Transcription factor that acts as a molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis.	MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis.2009 · DOI: 10.1093/pcp/pcp139 MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes.2012 · DOI: 10.1093/pcp/pcr185
`At5g12870`	Transcription activator.	The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis.2007 · DOI: 10.1105/tpc.107.053678 MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis.2009 · DOI: 10.1093/pcp/pcp139 MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes.2012 · DOI: 10.1093/pcp/pcr185 Transcription factor MYB46 is an obligate component of the transcriptional regulatory complex for functional expression of secondary wall-associated cellulose synthases in Arabidopsis thaliana.2013 · DOI: 10.1016/j.jplph.2013.04.012 Transcription factors that directly regulate the expression of CSLA9 encoding mannan synthase in Arabidopsis thaliana.2014 · DOI: 10.1007/s11103-013-0154-9
`At5g26660`	Probable transcription factor.	No verified direct reference in this release
`At1g09540`	Transcription factor that coordinates a small network of downstream target genes required for several aspects of plant growth and development, such as xylem formation and xylem cell differentiation, and lateral root formation.	AtMYB61, an R2R3-MYB transcription factor controlling stomatal aperture in Arabidopsis thaliana.2005 · DOI: 10.1016/j.cub.2005.06.041 MUM ENHANCERS are important for seed coat mucilage production and mucilage secretory cell differentiation in Arabidopsis thaliana.2009 · DOI: 10.1093/jxb/erp102 AtMYB61, an R2R3-MYB transcription factor, functions as a pleiotropic regulator via a small gene network.2012 · DOI: 10.1111/j.1469-8137.2012.04201.x Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.2013 · DOI: 10.1371/journal.pone.0065132 AaMYB1 and its orthologue AtMYB61 affect terpene metabolism and trichome development in Artemisia annua and Arabidopsis thaliana.2017 · DOI: 10.1111/tpj.13509

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004438 · 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:0009834 plant-type secondary cell wall biogenesis Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010089 xylem development Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0010214 seed coat development Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

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

GO:0048364 root development Biological Process

GO:0050832 defense response to fungus Biological Process

GO:1901348 positive regulation of secondary cell wall biogenesis Biological Process

KEGG gene cross-reference

ath:AT1G09540

ath:AT3G08500

ath:AT5G12870

ath:AT5G26660

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.

Nucleus0.976

Rank 1 · LXL04_004438 · OH-1004

Cytoplasm0.091

Rank 2 · LXL04_004438 · OH-1004

Cell membrane0.022

Rank 3 · LXL04_004438 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_004438 · OH-1004

Plastid0.010

Rank 5 · LXL04_004438 · 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-binding19-66 aa

PF13921.13Myb_DNA-bind_622-81 aa

PF00249.38Myb_DNA-binding72-115 aa

PF13921.13Myb_DNA-bind_675-125 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004438	`PF00249.38`	Myb_DNA-binding	19	66	3.7e-34	117.3
LXL04_004438	`PF13921.13`	Myb_DNA-bind_6	22	81	4.1e-21	75.7
LXL04_004438	`PF00249.38`	Myb_DNA-binding	72	115	3.7e-34	117.3
LXL04_004438	`PF13921.13`	Myb_DNA-bind_6	75	125	4.1e-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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9C6U1`	Arabidopsis thaliana	Transcription factor MYB83	43.465%	Swiss-Prot	moderate database homology
`Q9LXV2`	Arabidopsis thaliana	Transcription factor MYB46	50.206%	Swiss-Prot	strong database homology
`Q8LPH6`	Arabidopsis thaliana	Transcription factor MYB86	68.548%	Swiss-Prot	weak database homology
`Q8VZQ2`	Arabidopsis thaliana	Transcription factor MYB61	72.414%	Swiss-Prot	weak database homology

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