LXL04_030392 | RubberDandelionOmics

Gene overview

LXL04_030392

Reference: OH-1004 Chr: Chr06 Coordinates: 115195306-115196888 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1188 bp · LXL04_030392|LXL04_030392|OH1004|cDNA

ATGTTTCTCAATAACACCATCTCCCAAAAACACACCTTTCACAACCTTTTctttcatcatcatcatcaaccTTCCACCCTTCCATCCAAATTCCCCACCAAGATGGAGTCTTTCGGAATCTTGTTTGATGAAGAATGGGAAAGTTTGAGCAGAATTTTATCCGATGATCAAGATTCCGGCCACTTTCCCGGCTACGATGATCGTGGTTTGAACTTTGATACTCATTCCATTGTTTCATCTTTTATGAGTACTCATGAAGC...

CDS

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1188 bp · LXL04_030392|LXL04_030392|OH1004|CDS

ATGTTTCTCAATAACACCATCTCCCAAAAACACACCTTTCACAACCTTTTCTTTCATCATCATCATCAACCTTCCACCCTTCCATCCAAATTCCCCACCAAGATGGAGTCTTTCGGAATCTTGTTTGATGAAGAATGGGAAAGTTTGAGCAGAATTTTATCCGATGATCAAGATTCCGGCCACTTTCCCGGCTACGATGATCGTGGTTTGAACTTTGATACTCATTCCATTGTTTCATCTTTTATGAGTACTCATGAAGC...

Protein

Download Protein FASTA

395 aa · LXL04_030392|LXL04_030392|OH1004|PROTEIN

MFLNNTISQKHTFHNLFFHHHHQPSTLPSKFPTKMESFGILFDEEWESLSRILSDDQDSGHFPGYDDRGLNFDTHSIVSSFMSTHEANQNNSSFINDHGSYYDHATENMNPNLSHYFSQESNNNGCAHYDHGAASLPLLTNGNVSNHESMDLYDENDYHSTLLAQVFSDDSMEELLCSRKEVINVENYTVDPSVPIADKNMNKNTVPSKRKIEILESPNEVEEKVNIEEPNENPKKKTRKNKKKAQPKKKQKVMNATVNN...

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_030392`
TK1151 ID	TkA07G401050
OH-1004 ID	LXL04_030392
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.800
Protein coverage (%)	TK1151 100.000 / OH-1004 91.392 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_030392

Location Chr06:115195306-115196888 (-)

Description Similar to BHLH84: Transcription factor bHLH84

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g14760`	Transcription factor bHLH84.	No verified direct reference in this release
`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
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_030392 · 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.

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.

Nucleus0.978

Rank 1 · LXL04_030392 · OH-1004

Cytoplasm0.084

Rank 2 · LXL04_030392 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_030392 · OH-1004

Endoplasmic reticulum0.020

Rank 4 · LXL04_030392 · OH-1004

Plastid0.011

Rank 5 · LXL04_030392 · 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.

PF00010.32HLH320-360 aa

PF23173.3bHLH_SAC51320-363 aa

PF23176.1bHLH_LHW322-360 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030392	`PF00010.32`	HLH	320	360	1.9e-09	37.9
LXL04_030392	`PF23173.3`	bHLH_SAC51	320	363	7.9e-07	29.6
LXL04_030392	`PF23176.1`	bHLH_LHW	322	360	1.3e-06	29.0

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
`Q7XHI9`	Arabidopsis thaliana	Transcription factor bHLH84	57.627%	Swiss-Prot	weak database homology
`Q84WK0`	Arabidopsis thaliana	Transcription factor RSL2	57.303%	Swiss-Prot	weak database homology
`Q8LEG1`	Arabidopsis thaliana	Transcription factor RSL3	60.959%	Swiss-Prot	weak database homology
`Q3E7L7`	Arabidopsis thaliana	Transcription factor bHLH139	54.422%	Swiss-Prot	weak database homology
`Q2QQ32`	Oryza sativa subsp. japonica	Transcription factor BHLH133	69.048%	Swiss-Prot	weak database homology

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