LXL04_011962 | RubberDandelionOmics

Gene overview

LXL04_011962

Reference: OH-1004 Chr: Chr03 Coordinates: 3741517-3742161 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

645 bp · LXL04_011962|LXL04_011962|OH1004|cDNA

ATGACTACTATTATTCGATTCAATACGCCGTACTCCACAGTACAGTCAGCTGAATCTTGTTCAACTTCTGATTGCAGCACCACCGGAAGCTTTTCCGACGAGGAGGTCATGTTAGCTTCAAAAAACCCCAAGAAGCGAGCTGGGAGGAAGAAGTTCAAAGAGACACGCCACCCAGTTTACCGGGGAGTGCGCCGGAGAAATTCCGGCAAATGGGTGTGCGAGGTCAGAGAGCCCAATAAGAAAACCAGGATGTGGCTGGG...

CDS

Download CDS FASTA

645 bp · LXL04_011962|LXL04_011962|OH1004|CDS

ATGACTACTATTATTCGATTCAATACGCCGTACTCCACAGTACAGTCAGCTGAATCTTGTTCAACTTCTGATTGCAGCACCACCGGAAGCTTTTCCGACGAGGAGGTCATGTTAGCTTCAAAAAACCCCAAGAAGCGAGCTGGGAGGAAGAAGTTCAAAGAGACACGCCACCCAGTTTACCGGGGAGTGCGCCGGAGAAATTCCGGCAAATGGGTGTGCGAGGTCAGAGAGCCCAATAAGAAAACCAGGATGTGGCTGGG...

Protein

Download Protein FASTA

214 aa · LXL04_011962|LXL04_011962|OH1004|PROTEIN

MTTIIRFNTPYSTVQSAESCSTSDCSTTGSFSDEEVMLASKNPKKRAGRKKFKETRHPVYRGVRRRNSGKWVCEVREPNKKTRMWLGTYLTADMAARAHDVAALALKGRSACLNFADSVWRLPVPESSNVQDIKKVALEAAEAFRPPESDVAEVEESKELTVNCLYMDEEEIFGMPGFLANMAEGLMLPPPMTVGYDNYEDDVEFSFDSSLWSF

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_011962`
TK1151 ID	TkA02G600430
OH-1004 ID	LXL04_011962
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	78.500
Protein coverage (%)	TK1151 100.000 / OH-1004 83.178 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_011962

Location Chr03:3741517-3742161 (+)

Description Similar to DREB1C: Dehydration-responsive element-binding protein 1C

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g25470`	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'.	Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis.2005 · DOI: 10.1104/pp.105.068510
`At5g51990`	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'.	Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis.2002 · DOI: 10.1104/pp.006478
`At4g25480`	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'.	DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression.2002 · DOI: 10.1006/bbrc.2001.6299 Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis.2005 · DOI: 10.1104/pp.105.068510
`At4g25490`	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'.	Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis.2005 · DOI: 10.1104/pp.105.068510
`At1g63030`	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011962 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009631 cold acclimation Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0010371 regulation of gibberellin biosynthetic process Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0019760 glucosinolate metabolic process Biological Process

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

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

KEGG gene cross-reference

ath:AT1G63030

ath:AT4G25470

ath:AT4G25480

ath:AT4G25490

ath:AT5G51990

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.

Nucleus0.955

Rank 1 · LXL04_011962 · OH-1004

Cytoplasm0.115

Rank 2 · LXL04_011962 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_011962 · OH-1004

Endoplasmic reticulum0.020

Rank 4 · LXL04_011962 · OH-1004

Plastid0.017

Rank 5 · LXL04_011962 · 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.

PF00847.27AP258-108 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011962	`PF00847.27`	AP2	58	108	8.6e-14	52.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9SYS6`	Arabidopsis thaliana	Dehydration-responsive element-binding protein 1C	55.610%	Swiss-Prot	strong database homology
`Q9FJ93`	Arabidopsis thaliana	Dehydration-responsive element-binding protein 1D	57.732%	Swiss-Prot	strong database homology
`Q9M0L0`	Arabidopsis thaliana	Dehydration-responsive element-binding protein 1A	58.209%	Swiss-Prot	strong database homology
`P93835`	Arabidopsis thaliana	Dehydration-responsive element-binding protein 1B	60.526%	Swiss-Prot	strong database homology
`Q9SGJ6`	Arabidopsis thaliana	Dehydration-responsive element-binding protein 1E	51.337%	Swiss-Prot	strong database homology

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