LXL04_027159 | RubberDandelionOmics

Gene overview

LXL04_027159

Reference: OH-1004 Chr: Chr06 Coordinates: 9811909-9812925 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

630 bp · LXL04_027159|LXL04_027159|OH1004|cDNA

ATGGAGTTTTATGATGATATATCATCCGTTGTGGAAGAAACCAACGGTATGCTTTGTAGAAACAGGAAGCGGAATTATGATGGAGATGATGATGATAACAACGATGAGGATGAAGGCAGATTCAAGTCCAAGAACCTCAAAGCTGAAAGGAAAAGACGCGAAAAACTCAAATCAAGAATGCTAGAATTACGATCTCTAGTTCCTAAAATAACAAATttgaacaaagaaacaatcatAACGGATGCTATTGATTACATTGA...

CDS

Download CDS FASTA

630 bp · LXL04_027159|LXL04_027159|OH1004|CDS

ATGGAGTTTTATGATGATATATCATCCGTTGTGGAAGAAACCAACGGTATGCTTTGTAGAAACAGGAAGCGGAATTATGATGGAGATGATGATGATAACAACGATGAGGATGAAGGCAGATTCAAGTCCAAGAACCTCAAAGCTGAAAGGAAAAGACGCGAAAAACTCAAATCAAGAATGCTAGAATTACGATCTCTAGTTCCTAAAATAACAAATTTGAACAAAGAAACAATCATAACGGATGCTATTGATTACATTGA...

Protein

Download Protein FASTA

209 aa · LXL04_027159|LXL04_027159|OH1004|PROTEIN

MEFYDDISSVVEETNGMLCRNRKRNYDGDDDDNNDEDEGRFKSKNLKAERKRREKLKSRMLELRSLVPKITNLNKETIITDAIDYIEELQDSVTNLTNEIHKIEAELAIEQSFDILHICQEEKMKKWGIESEVEVSRINENKLWMKIVFEKKVGGFTKLIQAMSMLGIELVDTSVTTTKGAVLVTSCIEGKMLIPEQVREELVDVIKVL

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_027159`
TK1151 ID	TkA07G035820
OH-1004 ID	LXL04_027159
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.000
Protein coverage (%)	TK1151 100.000 / OH-1004 92.344 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_027159

Location Chr06:9811909-9812925 (+)

Description Similar to DYT1: Transcription factor DYT1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21330`	Transcription factor.	Regulation of Arabidopsis tapetum development and function by DYSFUNCTIONAL TAPETUM1 (DYT1) encoding a putative bHLH transcription factor.2006 · DOI: 10.1242/dev.02463
`At2g16910`	Transcription factor.	No verified direct reference in this release
`At1g10610`	Transcription factor bHLH90.	No verified direct reference in this release
`At3g26744`	Transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes.	SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis.2007 · DOI: 10.1105/tpc.106.048397 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
`Os02g0120500`	Transcription factor involved in the regulation of tapetum programmed cell death (PCD) and degradation during male reproductive development.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027159 · 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:0009409 response to cold Biological Process

GO:0009555 pollen development Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009960 endosperm development Biological Process

GO:0010115 regulation of abscisic acid biosynthetic process Biological Process

GO:0010162 seed dormancy process Biological Process

GO:0010440 stomatal lineage progression Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

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

GO:0048317 seed morphogenesis Biological Process

KEGG gene cross-reference

ath:AT1G10610

ath:AT2G16910

ath:AT3G26744

ath:AT4G21330

dosa:Os02g0120500

osa:4328113

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.

Nucleus0.914

Rank 1 · LXL04_027159 · OH-1004

Cytoplasm0.177

Rank 2 · LXL04_027159 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_027159 · OH-1004

Endoplasmic reticulum0.019

Rank 4 · LXL04_027159 · OH-1004

Plastid0.009

Rank 5 · LXL04_027159 · 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.

PF00010.32HLH45-90 aa

PF23177.2bHLH_IRO347-106 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027159	`PF00010.32`	HLH	45	90	2e-09	37.8
LXL04_027159	`PF23177.2`	bHLH_IRO3	47	106	5.7e-06	27.3

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
`O81900`	Arabidopsis thaliana	Transcription factor DYT1	43.407%	Swiss-Prot	moderate database homology
`Q9ZVX2`	Arabidopsis thaliana	Transcription factor ABORTED MICROSPORES	28.788%	Swiss-Prot	weak database homology
`Q0WNR2`	Arabidopsis thaliana	Transcription factor bHLH90	36.552%	Swiss-Prot	moderate database homology
`Q9LSE2`	Arabidopsis thaliana	Transcription factor ICE1	28.261%	Swiss-Prot	weak database homology
`Q6YUS3`	Oryza sativa subsp. japonica	Transcription factor TDR	30.851%	Swiss-Prot	moderate database homology

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