LXL04_011885 | RubberDandelionOmics

Gene overview

LXL04_011885

Reference: OH-1004 Chr: Chr03 Coordinates: 2187078-2187849 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

705 bp · LXL04_011885|LXL04_011885|OH1004|cDNA

ATGAGGTGTAGTAGGTCTTCAGAGAAGACAAAGCTAATTCATAAGAAAGGGTTATGGTCGCCTGATGAAGATCAAAAGCTCAGAGATTACATCACAAACCATGGACATGGCTGCTGGAGTTCTGTCCCCATTCAGACAGGTCTGCAAAGAAACGGAAAGAGTTGCAGATTAAGATGGATTAATTATCTACGGCCAGGATTGAAAAGAGGAACCTTCACCTCACATGAAGAGGACATCGTTCTCTCTCTTCATGCCACTTT...

CDS

Download CDS FASTA

705 bp · LXL04_011885|LXL04_011885|OH1004|CDS

ATGAGGTGTAGTAGGTCTTCAGAGAAGACAAAGCTAATTCATAAGAAAGGGTTATGGTCGCCTGATGAAGATCAAAAGCTCAGAGATTACATCACAAACCATGGACATGGCTGCTGGAGTTCTGTCCCCATTCAGACAGGTCTGCAAAGAAACGGAAAGAGTTGCAGATTAAGATGGATTAATTATCTACGGCCAGGATTGAAAAGAGGAACCTTCACCTCACATGAAGAGGACATCGTTCTCTCTCTTCATGCCACTTT...

Protein

Download Protein FASTA

234 aa · LXL04_011885|LXL04_011885|OH1004|PROTEIN

MRCSRSSEKTKLIHKKGLWSPDEDQKLRDYITNHGHGCWSSVPIQTGLQRNGKSCRLRWINYLRPGLKRGTFTSHEEDIVLSLHATLGNKWSQMSQHLPGRTDNEIKNHWHSHLKKKVLNLTIAMKSQDIQTLSYTRTDSSLESSEADGCRNLPKVLFADWLSLEQFHNLDASGNDDMCRYTIGSQNTVTNSELLNEGSSYGFAESDFYDLISEDNISQNFNNSAVTLYSCDEL

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_011885`
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_011885

Location Chr03:2187078-2187849 (+)

Description Similar to LAF1: Transcription factor LAF1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g25560`	Transcription factor that promotes photomorphogenesis in the light by participating in the transmission of phytochrome A (phyA) signals to downstream responses.	LAF1, a MYB transcription activator for phytochrome A signaling.2001 · DOI: 10.1101/gad.915001 FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis transcription factors LAF1 and HFR1 to transmit phytochrome A signals for inhibition of hypocotyl elongation.2009 · DOI: 10.1105/tpc.109.067215
`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
`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
`At5g65230`	Probable transcription factor.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011885 · 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:0009585 red, far-red light phototransduction Biological Process

GO:0009639 response to red or far red light Biological Process

GO:0010018 far-red light signaling pathway Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010089 xylem development Biological Process

GO:0010091 trichome branching 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

KEGG gene cross-reference

ath:AT1G09540

ath:AT3G01140

ath:AT4G25560

ath:AT5G26660

ath:AT5G65230

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.

Nucleus0.910

Rank 1 · LXL04_011885 · OH-1004

Cytoplasm0.216

Rank 2 · LXL04_011885 · OH-1004

Mitochondrion0.023

Rank 3 · LXL04_011885 · OH-1004

Cell membrane0.019

Rank 4 · LXL04_011885 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_011885 · 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-binding16-63 aa

PF13921.13Myb_DNA-bind_619-77 aa

PF00249.38Myb_DNA-binding69-114 aa

PF13921.13Myb_DNA-bind_672-118 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011885	`PF00249.38`	Myb_DNA-binding	16	63	3.9e-31	107.6
LXL04_011885	`PF13921.13`	Myb_DNA-bind_6	19	77	3.5e-20	72.6
LXL04_011885	`PF00249.38`	Myb_DNA-binding	69	114	3.9e-31	107.6
LXL04_011885	`PF13921.13`	Myb_DNA-bind_6	72	118	3.5e-20	72.6

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
`Q9M0K4`	Arabidopsis thaliana	Transcription factor LAF1	48.108%	Swiss-Prot	moderate database homology
`Q8LPH6`	Arabidopsis thaliana	Transcription factor MYB86	58.993%	Swiss-Prot	moderate database homology
`Q8VZQ2`	Arabidopsis thaliana	Transcription factor MYB61	70.192%	Swiss-Prot	weak database homology
`Q9LE63`	Arabidopsis thaliana	Transcription factor MYB106	62.385%	Swiss-Prot	weak database homology
`Q9FJP2`	Arabidopsis thaliana	Transcription factor MYB53	60.331%	Swiss-Prot	moderate database homology

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