LXL04_006947 | RubberDandelionOmics

Gene overview

LXL04_006947

Reference: OH-1004 Chr: Chr02 Coordinates: 31368047-31369341 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

960 bp · LXL04_006947|LXL04_006947|OH1004|cDNA

ATGATGCAACAACCAAGCGGTCAACAAGGTCTCCTCCAAGATCTCTTGCCACCATTTACAGAAACTTGGTCGACATATCAAAATCCTCAAGAACTTTCCGCCATTGACACTCAATTATTCCCATCTCAAGAACATGATTTTCTGTTAttaccttcttcttcttcttctccctcATACATGCAACTCATCTCCTCCCCTATACAACCCACATTCCAATCGCTTTACAACGATGAATCAATCTACTGTTTTGATTCCTTCAC...

CDS

Download CDS FASTA

960 bp · LXL04_006947|LXL04_006947|OH1004|CDS

ATGATGCAACAACCAAGCGGTCAACAAGGTCTCCTCCAAGATCTCTTGCCACCATTTACAGAAACTTGGTCGACATATCAAAATCCTCAAGAACTTTCCGCCATTGACACTCAATTATTCCCATCTCAAGAACATGATTTTCTGTTATTACCTTCTTCTTCTTCTTCTCCCTCATACATGCAACTCATCTCCTCCCCTATACAACCCACATTCCAATCGCTTTACAACGATGAATCAATCTACTGTTTTGATTCCTTCAC...

Protein

Download Protein FASTA

319 aa · LXL04_006947|LXL04_006947|OH1004|PROTEIN

MMQQPSGQQGLLQDLLPPFTETWSTYQNPQELSAIDTQLFPSQEHDFLLLPSSSSSPSYMQLISSPIQPTFQSLYNDESIYCFDSFTPLNDSISPSYDHQLMVPLMAEEEEEDDDDRDGCQNAGSHDQISTVFTMGSNGEKKSNKSKKVEGQPSKNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILGDTIDYMKELLERINNLKEQDIESDVDARFKKFNMNESQARNPPKFNVERGNTDTQIHICCSTKPGLLLS...

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_006947`
TK1151 ID	TkA03G094840
OH-1004 ID	LXL04_006947
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_006947

Location Chr02:31368047-31369341 (-)

Description Similar to BHLH93: Transcription factor bHLH93

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g65640`	Transcription factor.	No verified direct reference in this release
`At5g10570`	Transcription factor bHLH61.	No verified direct reference in this release
`At1g12860`	Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.	SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation.2008 · DOI: 10.1105/tpc.108.060848

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0135700`	Transcription factor involved in defense responses that functions downstream of RAC1 and upstream of PAL1 and WRKY19 genes.	The bHLH Rac Immunity1 (RAI1) Is Activated by OsRac1 via OsMAPK3 and OsMAPK6 in Rice Immunity.2012 · DOI: 10.1093/pcp/pcs033
`Os10g0544200`	Probable transcription factor.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006947 · 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:0010371 regulation of gibberellin biosynthetic process Biological Process

GO:0010444 guard mother cell differentiation Biological Process

GO:0031347 regulation of defense response Biological Process

GO:0045487 gibberellin catabolic process Biological Process

GO:0050826 response to freezing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT1G12860

ath:AT5G10570

ath:AT5G65640

dosa:Os03g0135700

dosa:Os10g0544200

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.966

Rank 1 · LXL04_006947 · OH-1004

Cytoplasm0.117

Rank 2 · LXL04_006947 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_006947 · OH-1004

Endoplasmic reticulum0.021

Rank 4 · LXL04_006947 · OH-1004

Plastid0.012

Rank 5 · LXL04_006947 · 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.

PF00010.32HLH158-200 aa

PF23177.2bHLH_IRO3158-211 aa

PF22754.5bHLH-TF_ACT-like_plant237-308 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006947	`PF00010.32`	HLH	158	200	2.9e-10	40.5
LXL04_006947	`PF23177.2`	bHLH_IRO3	158	211	1.2e-06	29.5
LXL04_006947	`PF22754.5`	bHLH-TF_ACT-like_plant	237	308	7.2e-09	36.4

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
`Q9LSL1`	Arabidopsis thaliana	Transcription factor bHLH93	65.000%	Swiss-Prot	moderate database homology
`Q9LXA9`	Arabidopsis thaliana	Transcription factor bHLH61	62.963%	Swiss-Prot	moderate database homology
`Q9LPW3`	Arabidopsis thaliana	Transcription factor SCREAM2	47.568%	Swiss-Prot	moderate database homology
`Q10S44`	Oryza sativa subsp. japonica	Transcription factor BHLH3	62.778%	Swiss-Prot	moderate database homology
`Q336V8`	Oryza sativa subsp. japonica	Basic helix-loop-helix protein 004	52.660%	Swiss-Prot	moderate database homology

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