LXL04_006930 | RubberDandelionOmics

Gene overview

LXL04_006930

Reference: OH-1004 Chr: Chr02 Coordinates: 30272483-30273711 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

900 bp · LXL04_006930|LXL04_006930|OH1004|cDNA

ATGGATCTGTCACCGACATGGTTACCAGAGATGGAAATGGAAGATACAGTCATGAATTATGATCAAATGAGCGAGCTTTATGACACGGTTGATGACTTCAGCTTTGATTTTTTCACTTCAGAACCCAATACAGAAAACTTGACCCAATCTTTTCAAAAAACATGCACTAATACTATCAAGAAACGTTCTCCAACCCCAGAAGCCCTAATTACTACTTCTCTTTCATCATCCAAAACGTTCACCATATCTTTTGGAGGAGA...

CDS

Download CDS FASTA

900 bp · LXL04_006930|LXL04_006930|OH1004|CDS

ATGGATCTGTCACCGACATGGTTACCAGAGATGGAAATGGAAGATACAGTCATGAATTATGATCAAATGAGCGAGCTTTATGACACGGTTGATGACTTCAGCTTTGATTTTTTCACTTCAGAACCCAATACAGAAAACTTGACCCAATCTTTTCAAAAAACATGCACTAATACTATCAAGAAACGTTCTCCAACCCCAGAAGCCCTAATTACTACTTCTCTTTCATCATCCAAAACGTTCACCATATCTTTTGGAGGAGA...

Protein

Download Protein FASTA

299 aa · LXL04_006930|LXL04_006930|OH1004|PROTEIN

MDLSPTWLPEMEMEDTVMNYDQMSELYDTVDDFSFDFFTSEPNTENLTQSFQKTCTNTIKKRSPTPEALITTSLSSSKTFTISFGGDLKPKKEILHVHDHSLGATKIPTISRNPFQAQDHVLAERKRREKLNQHFISISSLLPNLKKMDKASVLEDAANYIKELQSRVKELEGLSGAKRKNAEEYVISIKKSKQLSSSDDEYTSSDESNSGESTDLCNLSPEIEVRMSGSSVLVRIQCQKNYSSFVKALTQIQNLGLSII...

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_006930`
TK1151 ID	TkA03G090040
OH-1004 ID	LXL04_006930
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_006930

Location Chr02:30272483-30273711 (+)

Description Similar to BHLH25: Transcription factor bHLH25

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g37850`	Transcription factor bHLH25.	No verified direct reference in this release
`At2g22750`	Transcription factor bHLH18.	No verified direct reference in this release
`At2g22770`	Transcription activator that regulates the expression of at least NAI2, PYK10 and PBP1.	A novel ER-derived compartment, the ER body, selectively accumulates a beta-glucosidase with an ER-retention signal in Arabidopsis.2003 · DOI: 10.1046/j.1365-313x.2003.01636.x NAI1 gene encodes a basic-helix-loop-helix-type putative transcription factor that regulates the formation of an endoplasmic reticulum-derived structure, the ER body.2004 · DOI: 10.1105/tpc.021154 Activation of an ER-body-localized beta-glucosidase via a cytosolic binding partner in damaged tissues of Arabidopsis thaliana.2005 · DOI: 10.1093/pcp/pci126 PYK10, a beta-glucosidase located in the endoplasmatic reticulum, is crucial for the beneficial interaction between Arabidopsis thaliana and the endophytic fungus Piriformospora indica.2008 · DOI: 10.1111/j.1365-313x.2008.03424.x Antagonistic jacalin-related lectins regulate the size of ER body-type beta-glucosidase complexes in Arabidopsis thaliana.2008 · DOI: 10.1093/pcp/pcn075 NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana.2008 · DOI: 10.1105/tpc.108.059345
`At2g22760`	Transcription factor bHLH19.	No verified direct reference in this release
`At5g46760`	Transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation.	The bHLH transcription factor MYC3 interacts with the Jasmonate ZIM-domain proteins to mediate jasmonate response in Arabidopsis.2011 · DOI: 10.1093/mp/ssq073 Characterization of JAZ-interacting bHLH transcription factors that regulate jasmonate responses in Arabidopsis.2011 · DOI: 10.1093/jxb/erq408 The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses.2011 · DOI: 10.1105/tpc.110.080788 Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior.2013 · DOI: 10.1105/tpc.113.115139

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006930 · 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:0006952 defense response Biological Process

GO:0007029 endoplasmic reticulum organization Biological Process

GO:0009718 anthocyanin-containing compound biosynthetic process Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0010374 stomatal complex development Biological Process

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

GO:0106167 extracellular ATP signaling Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G22750

ath:AT2G22760

ath:AT2G22770

ath:AT4G37850

ath:AT5G46760

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.

Nucleus0.969

Rank 1 · LXL04_006930 · OH-1004

Cytoplasm0.115

Rank 2 · LXL04_006930 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_006930 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_006930 · OH-1004

Plastid0.011

Rank 5 · LXL04_006930 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00010.32HLH119-165 aa

PF23177.2bHLH_IRO3122-173 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006930	`PF00010.32`	HLH	119	165	7.6e-12	45.6
LXL04_006930	`PF23177.2`	bHLH_IRO3	122	173	6.9e-09	36.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9T072`	Arabidopsis thaliana	Transcription factor bHLH25	43.147%	Swiss-Prot	moderate database homology
`Q1PF17`	Arabidopsis thaliana	Transcription factor bHLH18	43.147%	Swiss-Prot	moderate database homology
`Q8S3F1`	Arabidopsis thaliana	Transcription factor NAI1	37.949%	Swiss-Prot	moderate database homology
`Q1PF16`	Arabidopsis thaliana	Transcription factor bHLH19	38.947%	Swiss-Prot	moderate database homology
`Q9FIP9`	Arabidopsis thaliana	Transcription factor MYC3	36.496%	Swiss-Prot	weak database homology

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