LXL04_025779 | RubberDandelionOmics

Gene overview

LXL04_025779

Reference: OH-1004 Chr: Chr05 Coordinates: 116838270-116840010 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1143 bp · LXL04_025779|LXL04_025779|OH1004|cDNA

ATGTTTTCACCTGCTGCAAAACCTCAAGCGATCAATTTTTACCCACCACAAGAAACAATCATGATGATGGAATCCACCTCCACCCCTCACCACCACCAAACCCAAATGATCATTTCCGCTCCGGTTGCCGGCGGCGACACCACCAGCAGCGAAGAAAACACCATCAAGTCCTCAACCGCGACAACCTCAGCACCAGTGAAGAAACGAGCCGAGACTTGGGTCAAAGAAGAAACTCGAACCCTAATCCTCCTTCGCCACGA...

CDS

Download CDS FASTA

1143 bp · LXL04_025779|LXL04_025779|OH1004|CDS

ATGTTTTCACCTGCTGCAAAACCTCAAGCGATCAATTTTTACCCACCACAAGAAACAATCATGATGATGGAATCCACCTCCACCCCTCACCACCACCAAACCCAAATGATCATTTCCGCTCCGGTTGCCGGCGGCGACACCACCAGCAGCGAAGAAAACACCATCAAGTCCTCAACCGCGACAACCTCAGCACCAGTGAAGAAACGAGCCGAGACTTGGGTCAAAGAAGAAACTCGAACCCTAATCCTCCTTCGCCACGA...

Protein

Download Protein FASTA

380 aa · LXL04_025779|LXL04_025779|OH1004|PROTEIN

MFSPAAKPQAINFYPPQETIMMMESTSTPHHHQTQMIISAPVAGGDTTSSEENTIKSSTATTSAPVKKRAETWVKEETRTLILLRHEIDSLFNTSKSNKHLWDQISMKMREKGFDRSPTMCTDKWRNLLKEFKKAKEQNNGVSHNGYSANSKMQFYKEVEDVIRDRNKNSKVDSFMQFSDKGVDDTGITFGPVEANPRDALNLERRLDQEGHPLAITGADTMAATGVSPWNWRENPGNGDQNNTYGGRVISVKLGDYTRR...

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_025779`
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_025779

Location Chr05:116838270-116840010 (-)

Description Similar to GT-1: Trihelix transcription factor GT-1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g13450`	Probable transcription factor that binds specifically to the core DNA sequence 5'-GGTTAA-3'.	No verified direct reference in this release
`At3g25990`	Probable transcription factor that binds specific DNA sequence.	No verified direct reference in this release
`At2g38250`	Probable transcription factor that may play a role in the induction of CAM4 in response to pathogen and salt.	Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor.2004 · DOI: 10.1104/pp.104.041442
`At1g76880`	Transcription repressor that negatively regulates root hair growth by directly binding RSL4 promoter and repressing RSL4 expression.	No verified direct reference in this release
`At5g01380`	Probable transcription factor that binds specifically to the core DNA sequence 5'-GTTAC-3'.	Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis.2004 · DOI: 10.1016/s0014-5793(04)00222-4

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025779 · 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:0019760 glucosinolate metabolic process Biological Process

GO:0048354 mucilage biosynthetic process involved in seed coat development Biological Process

GO:0048358 mucilage pectin biosynthetic process Biological Process

GO:0048768 root hair cell tip growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0016592 mediator complex Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0000987 cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G13450

ath:AT1G76880

ath:AT2G38250

ath:AT3G25990

ath:AT5G01380

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.

Nucleus0.965

Rank 1 · LXL04_025779 · OH-1004

Cytoplasm0.085

Rank 2 · LXL04_025779 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_025779 · OH-1004

Endoplasmic reticulum0.022

Rank 4 · LXL04_025779 · OH-1004

Plastid0.015

Rank 5 · LXL04_025779 · 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.

PF13837.13Myb_DNA-bind_472-161 aa

PF26214.1Ubiquitin_GT-1248-308 aa

PF26214.1Ubiquitin_GT-1313-378 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025779	`PF13837.13`	Myb_DNA-bind_4	72	161	3.1e-21	76.3
LXL04_025779	`PF26214.1`	Ubiquitin_GT-1	248	308	5.6e-43	145.4
LXL04_025779	`PF26214.1`	Ubiquitin_GT-1	313	378	5.6e-43	145.4

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FX53`	Arabidopsis thaliana	Trihelix transcription factor GT-1	62.687%	Swiss-Prot	strong database homology
`Q9LU92`	Arabidopsis thaliana	Trihelix transcription factor GT-4	55.409%	Swiss-Prot	strong database homology
`O80450`	Arabidopsis thaliana	Trihelix transcription factor GT-3b	33.571%	Swiss-Prot	weak database homology
`Q9C6K3`	Arabidopsis thaliana	Trihelix transcription factor DF1	31.783%	Swiss-Prot	weak database homology
`Q9SDW0`	Arabidopsis thaliana	Trihelix transcription factor GT-3a	32.323%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card