LXL04_007953 | RubberDandelionOmics

Gene overview

LXL04_007953

Reference: OH-1004 Chr: Chr02 Coordinates: 77286484-77287921 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1065 bp · LXL04_007953|LXL04_007953|OH1004|cDNA

ATGGAAttttatgaaaattttattGATCAAGGATGGGTGAACATGAGCTCAATGTTCTCCGGTGATCAAGACTCCAGCCATTTTACAAGCCATCGGTTGATCTCAGGGGAACATCGTCATGATTTGGATTCTATTCTTTGGGAAAGTCCCAATGAATCTAATAATTCCATCACATGTTCTATAGATGATCATGGTTTAGTCTATGGTTCGGATTATGATCTTAAACCTACTTTCTACAATTATTTCTCTCAAGAAAGTAG...

CDS

Download CDS FASTA

1065 bp · LXL04_007953|LXL04_007953|OH1004|CDS

ATGGAATTTTATGAAAATTTTATTGATCAAGGATGGGTGAACATGAGCTCAATGTTCTCCGGTGATCAAGACTCCAGCCATTTTACAAGCCATCGGTTGATCTCAGGGGAACATCGTCATGATTTGGATTCTATTCTTTGGGAAAGTCCCAATGAATCTAATAATTCCATCACATGTTCTATAGATGATCATGGTTTAGTCTATGGTTCGGATTATGATCTTAAACCTACTTTCTACAATTATTTCTCTCAAGAAAGTAG...

Protein

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354 aa · LXL04_007953|LXL04_007953|OH1004|PROTEIN

MEFYENFIDQGWVNMSSMFSGDQDSSHFTSHRLISGEHRHDLDSILWESPNESNNSITCSIDDHGLVYGSDYDLKPTFYNYFSQESSINPTDIFQFCNSETPTDNGCHQFKDLGMIEGDSTNLLFLAQVFSDDAMEEILCLKEDDEEMVKKGKIENSHCQAVPMKETPIKRKYQNLEDDGNGNTEIIDNRKKKSRVARDNKNKKNLPPMNKKMTSATNSNEDETKEKQLNNEDFTQNISSSCSEDDSNASQDVKEGPINV...

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_007953`
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_007953

Location Chr02:77286484-77287921 (-)

Description Similar to RSL2: Transcription factor RSL2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g33880`	Transcription factor involved in the regulation of root hair elongation.	A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate.2018 · DOI: 10.1038/s41467-018-03851-3
`At2g14760`	Transcription factor bHLH84.	No verified direct reference in this release
`At1g27740`	Transcription factor involved in the regulation of root hair elongation.	A basic helix-loop-helix transcription factor controls cell growth and size in root hairs.2010 · DOI: 10.1038/ng.529 Intensity of a pulse of RSL4 transcription factor synthesis determines Arabidopsis root hair cell size.2015 · DOI: 10.1038/nplants.2015.138 ROOT HAIR DEFECTIVE SIX-LIKE4 (RSL4) promotes root hair elongation by transcriptionally regulating the expression of genes required for cell growth.2016 · DOI: 10.1111/nph.14095 A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate.2018 · DOI: 10.1038/s41467-018-03851-3
`At5g43175`	Transcription factor bHLH139.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0508500`	Transcription factor that acts as a regulator of iron homeostasis.	Identification of OsbHLH133 as a regulator of iron distribution between roots and shoots in Oryza sativa.2013 · DOI: 10.1111/j.1365-3040.2012.02569.x

Functional annotation source

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Functional annotation source: OH1004 · LXL04_007953 · 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:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009555 pollen development Biological Process

GO:0009733 response to auxin Biological Process

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

GO:0048766 root hair initiation Biological Process

GO:0005634 nucleus Cellular Component

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT1G27740

ath:AT2G14760

ath:AT4G33880

ath:AT5G43175

osa:107276670

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.

Nucleus0.976

Rank 1 · LXL04_007953 · OH-1004

Cytoplasm0.088

Rank 2 · LXL04_007953 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_007953 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_007953 · OH-1004

Plastid0.011

Rank 5 · LXL04_007953 · 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.

PF00010.32HLH280-320 aa

PF23173.3bHLH_SAC51280-325 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007953	`PF00010.32`	HLH	280	320	1.6e-08	34.9
LXL04_007953	`PF23173.3`	bHLH_SAC51	280	325	6.3e-08	33.1

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
`Q84WK0`	Arabidopsis thaliana	Transcription factor RSL2	44.493%	Swiss-Prot	moderate database homology
`Q7XHI9`	Arabidopsis thaliana	Transcription factor bHLH84	71.552%	Swiss-Prot	weak database homology
`Q8LEG1`	Arabidopsis thaliana	Transcription factor RSL3	57.333%	Swiss-Prot	weak database homology
`Q3E7L7`	Arabidopsis thaliana	Transcription factor bHLH139	61.739%	Swiss-Prot	weak database homology
`Q2QQ32`	Oryza sativa subsp. japonica	Transcription factor BHLH133	59.223%	Swiss-Prot	weak database homology

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