LXL04_026301 | RubberDandelionOmics

Gene overview

LXL04_026301

Reference: OH-1004 Chr: Chr05 Coordinates: 124657936-124662247 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1962 bp · LXL04_026301|LXL04_026301|OH1004|cDNA

ATGGATAATCGCGGTTCATCTTTTCTCTCACCTGAAGATCTGCTGTATAAGGAGCTATGGAAGGCATGTGCGGGCCCACTAGTGGATGTTCCAAGAGACGGAGAAAAAGTTTTCTACTTTCCTCAAGGCCACATGGAACAATTAGAGGCATCAACAAATCAGGAATTAAATCTGCGGATTCCTCTCTTCAACCTCAATTCAAAGATTCTTTGTCGTGTTGTTCATACTCAGCTTATGGCCGAACAAGACACCGATGAAGT...

CDS

Download CDS FASTA

1962 bp · LXL04_026301|LXL04_026301|OH1004|CDS

ATGGATAATCGCGGTTCATCTTTTCTCTCACCTGAAGATCTGCTGTATAAGGAGCTATGGAAGGCATGTGCGGGCCCACTAGTGGATGTTCCAAGAGACGGAGAAAAAGTTTTCTACTTTCCTCAAGGCCACATGGAACAATTAGAGGCATCAACAAATCAGGAATTAAATCTGCGGATTCCTCTCTTCAACCTCAATTCAAAGATTCTTTGTCGTGTTGTTCATACTCAGCTTATGGCCGAACAAGACACCGATGAAGT...

Protein

Download Protein FASTA

653 aa · LXL04_026301|LXL04_026301|OH1004|PROTEIN

MDNRGSSFLSPEDLLYKELWKACAGPLVDVPRDGEKVFYFPQGHMEQLEASTNQELNLRIPLFNLNSKILCRVVHTQLMAEQDTDEVYAQITLLPEIDQSDPTSPDECIAEPVKPTVHSFCKVLTASDTSTHGGFSVLRKHANECLPPLDMTQATPTQELSATDLHGTEWRFKHIFRGQPRRHLLTTGWSTFVTNKRLMAGDSFVFLRGENGELRVGVRRQARQQTSMPSSVISSQSMHLGVLATASHAVSTQTRFAVYY...

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_026301`
TK1151 ID	TkA06G015390
OH-1004 ID	LXL04_026301
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	97.100
Protein coverage (%)	TK1151 97.347 / OH-1004 74.273 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

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_026301

Location Chr05:124657936-124662247 (-)

Description Similar to ARF9: Auxin response factor 9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g23980`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release
`At3g61830`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release
`At2g46530`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release
`At1g59750`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0557200`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026301 · 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:0008219 cell death Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0010150 leaf senescence Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G59750

ath:AT2G46530

ath:AT3G61830

ath:AT4G23980

dosa:Os02g0557200

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.

Nucleus0.963

Rank 1 · LXL04_026301 · OH-1004

Cytoplasm0.088

Rank 2 · LXL04_026301 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_026301 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_026301 · OH-1004

Plastid0.015

Rank 5 · LXL04_026301 · 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.

PF02362.27B3120-221 aa

PF25313.2BRWD_AD274-357 aa

PF06507.20ARF_AD277-358 aa

PF02309.23AUX_IAA527-582 aa

PF02309.23AUX_IAA587-630 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026301	`PF02362.27`	B3	120	221	1.1e-23	83.8
LXL04_026301	`PF25313.2`	BRWD_AD	274	357	5.4e-10	40.2
LXL04_026301	`PF06507.20`	ARF_AD	277	358	5.6e-35	119.8
LXL04_026301	`PF02309.23`	AUX_IAA	527	582	6.1e-14	53.1
LXL04_026301	`PF02309.23`	AUX_IAA	587	630	6.1e-14	53.1

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
`Q9XED8`	Arabidopsis thaliana	Auxin response factor 9	58.559%	Swiss-Prot	strong database homology
`Q9C5W9`	Arabidopsis thaliana	Auxin response factor 18	57.729%	Swiss-Prot	strong database homology
`Q9ZPY6`	Arabidopsis thaliana	Auxin response factor 11	56.808%	Swiss-Prot	strong database homology
`Q8L7G0`	Arabidopsis thaliana	Auxin response factor 1	51.897%	Swiss-Prot	strong database homology
`Q6YVY0`	Oryza sativa subsp. japonica	Auxin response factor 7	52.194%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card