LXL04_031241 | RubberDandelionOmics

Gene overview

LXL04_031241

Reference: OH-1004 Chr: Chr07 Coordinates: 3029889-3031240 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

984 bp · LXL04_031241|LXL04_031241|OH1004|cDNA

ATGATGGATCCAAAGTTCGCCGGGAACCCAATCCCCACTTCACCGTATTATGGTGGTGGTCGGACTGATATCGATCAGATGCCGGAAACGCCCAATCGCGGAAGCCACCACCGCCGGGCCATGTCGGAGACCTTCTTCCGGTTCCCAGACGAAGACATGCTACTAGACGACGTCGTTGCGGACTTCAACTTCGCCAATATAGACCTCCCATCGCTGTCCTGCGACGCTCCTGTACCTACCACAACGGAAGATTCTTGTAA...

CDS

Download CDS FASTA

984 bp · LXL04_031241|LXL04_031241|OH1004|CDS

ATGATGGATCCAAAGTTCGCCGGGAACCCAATCCCCACTTCACCGTATTATGGTGGTGGTCGGACTGATATCGATCAGATGCCGGAAACGCCCAATCGCGGAAGCCACCACCGCCGGGCCATGTCGGAGACCTTCTTCCGGTTCCCAGACGAAGACATGCTACTAGACGACGTCGTTGCGGACTTCAACTTCGCCAATATAGACCTCCCATCGCTGTCCTGCGACGCTCCTGTACCTACCACAACGGAAGATTCTTGTAA...

Protein

Download Protein FASTA

327 aa · LXL04_031241|LXL04_031241|OH1004|PROTEIN

MMDPKFAGNPIPTSPYYGGGRTDIDQMPETPNRGSHHRRAMSETFFRFPDEDMLLDDVVADFNFANIDLPSLSCDAPVPTTTEDSCKSDRESNDVNASKLTARKPLGYSSHIRSLSVGSDFFDGFGLSSAAEPEKLGGGGAYRHRHSSSMDGSPATSFEGDSVSMMLDNSKKALPPDKLAELSLIDPKRAKRILANRQSAARSKERKTRYTSELERKVQTLQTEATTLSAEVTKLQRDTSGLTSENKELKLRLEAMEQHA...

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_031241`
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_031241

Location Chr07:3029889-3031240 (+)

Description Similar to VIP1: Transcription factor VIP1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g43700`	Transcription activator that binds specifically to the VIP1 response elements (VREs) DNA sequence 5'-ACNGCT-3' found in some stress genes (e.g. TRX8 and MYB44), when phosphorylated/activated by MPK3.	Isolation and characterization of low-sulphur-tolerant mutants of Arabidopsis.2010 · DOI: 10.1093/jxb/erq161
`At2g31370`	Putative transcription factor with an activatory role.	No verified direct reference in this release
`At2g40620`	Transcription factor that may participate with bZIP34 in the gametophytic control of pollen development.	Characterization of pollen-expressed bZIP protein interactions and the role of ATbZIP18 in the male gametophyte.2017 · DOI: 10.1007/s00497-016-0295-5

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0336200`	Transcription factor probably involved in vascular development and shoot tissue organization.	RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease.2004 · DOI: 10.1073/pnas.0307687100
`Os09g0516200`	Transcription factor probably involved in vascular development and shoot tissue organization.	Transcription factor RF2a alters expression of the rice tungro bacilliform virus promoter in transgenic tobacco plants.2001 · DOI: 10.1073/pnas.121186398 Functional analysis of RF2a, a rice transcription factor.2003 · DOI: 10.1074/jbc.m304862200 RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease.2004 · DOI: 10.1073/pnas.0307687100 RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development.1997 · DOI: 10.1093/emboj/16.17.5247

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031241 · 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:0006970 response to osmotic stress Biological Process

GO:0007231 osmosensory signaling pathway Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009652 thigmotropism Biological Process

GO:0009970 cellular response to sulfate starvation Biological Process

GO:0045596 negative regulation of cell differentiation Biological Process

GO:0051170 import into nucleus Biological Process

GO:1902358 sulfate transmembrane transport Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G43700

ath:AT2G31370

ath:AT2G40620

dosa:Os03g0336200

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.

Nucleus0.973

Rank 1 · LXL04_031241 · OH-1004

Cytoplasm0.099

Rank 2 · LXL04_031241 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_031241 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_031241 · OH-1004

Plastid0.011

Rank 5 · LXL04_031241 · 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.

PF07716.21bZIP_2186-237 aa

PF00170.27bZIP_1188-247 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031241	`PF07716.21`	bZIP_2	186	237	3.8e-07	30.7
LXL04_031241	`PF00170.27`	bZIP_1	188	247	1.1e-10	42.2

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
`Q9MA75`	Arabidopsis thaliana	Transcription factor VIP1	46.313%	Swiss-Prot	moderate database homology
`Q04088`	Arabidopsis thaliana	Probable transcription factor PosF21	45.455%	Swiss-Prot	moderate database homology
`O22873`	Arabidopsis thaliana	bZIP transcription factor 18	46.360%	Swiss-Prot	moderate database homology
`Q6S4P4`	Oryza sativa subsp. japonica	Transcription factor RF2b	43.945%	Swiss-Prot	moderate database homology
`Q69IL4`	Oryza sativa subsp. japonica	Transcription factor RF2a	62.838%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card