LXL04_013932 | RubberDandelionOmics

Gene overview

LXL04_013932

Reference: OH-1004 Chr: Chr03 Coordinates: 38352386-38356993 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2691 bp · LXL04_013932|LXL04_013932|OH1004|cDNA

ATGGTCGCACATGCCTACTGTCATGTCACTCCAAAATCAACGGTTACGATCTCCAGGTCGCCTACGGTCGGGCCGGGTGCCGTGTATAAAAGCTCCCTGCGTCACCCTCAATAtttctttttccttttttctattttttatcAGCTCGATAGTGATTGGGGGGAAAAGTTGGAAAGAGAAGGGTTTTTCATGGCGGTGTTcgggaagaagaagaagaatcagtGGTTTGCTGAGCTGGGGTTTACATATAATATGAAGCT...

CDS

Download CDS FASTA

2691 bp · LXL04_013932|LXL04_013932|OH1004|CDS

ATGGTCGCACATGCCTACTGTCATGTCACTCCAAAATCAACGGTTACGATCTCCAGGTCGCCTACGGTCGGGCCGGGTGCCGTGTATAAAAGCTCCCTGCGTCACCCTCAATATTTCTTTTTCCTTTTTTCTATTTTTTATCAGCTCGATAGTGATTGGGGGGAAAAGTTGGAAAGAGAAGGGTTTTTCATGGCGGTGTTCGGGAAGAAGAAGAAGAATCAGTGGTTTGCTGAGCTGGGGTTTACATATAATATGAAGCT...

Protein

Download Protein FASTA

896 aa · LXL04_013932|LXL04_013932|OH1004|PROTEIN

MVAHAYCHVTPKSTVTISRSPTVGPGAVYKSSLRHPQYFFFLFSIFYQLDSDWGEKLEREGFFMAVFGKKKKNQWFAELGFTYNMKLSTSGLGQQPHEGEKKCLNSELWHACAGPLVSLPIVGSRVVYFPQGHSEQVAATTNKEIDAHIPNYPSLPPQLICQLHNVTMHADVETDEVYAQMTLQPLTPQEQKDTFLPVELGTPSRQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDFSQQPPAQELIARDLHDVE...

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_013932`
TK1151 ID	TkA02G463120
OH-1004 ID	LXL04_013932
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 90.625 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_013932

Location Chr03:38352386-38356993 (-)

Description Similar to ARF8: Auxin response factor 8

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g37020`	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).	Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation.2005 · DOI: 10.1242/dev.01955 AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis.2006 · DOI: 10.1105/tpc.105.037192

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q258Y5`	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
`Os04g0671900`	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
`Os02g0164900`	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
`UniProt: A2X1A1`	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_013932 · 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:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0010154 fruit development Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT5G37020

dosa:Os02g0164900

dosa:Os04g0671900

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.

Nucleus0.933

Rank 1 · LXL04_013932 · OH-1004

Cytoplasm0.116

Rank 2 · LXL04_013932 · OH-1004

Cell membrane0.037

Rank 3 · LXL04_013932 · OH-1004

Endoplasmic reticulum0.029

Rank 4 · LXL04_013932 · OH-1004

Plastid0.020

Rank 5 · LXL04_013932 · 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.

PF02362.27B3211-312 aa

PF25313.2BRWD_AD334-443 aa

PF06507.20ARF_AD360-443 aa

PF02309.23AUX_IAA826-868 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013932	`PF02362.27`	B3	211	312	2.5e-23	82.6
LXL04_013932	`PF25313.2`	BRWD_AD	334	443	5.1e-09	37.1
LXL04_013932	`PF06507.20`	ARF_AD	360	443	1.8e-34	118.2
LXL04_013932	`PF02309.23`	AUX_IAA	826	868	1.7e-09	38.5

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
`Q9FGV1`	Arabidopsis thaliana	Auxin response factor 8	67.037%	Swiss-Prot	strong database homology
`Q258Y5`	Oryza sativa subsp. indica	Auxin response factor 12	61.661%	Swiss-Prot	strong database homology
`Q0J951`	Oryza sativa subsp. japonica	Auxin response factor 12	61.585%	Swiss-Prot	strong database homology
`Q6H6V4`	Oryza sativa subsp. japonica	Auxin response factor 6	55.483%	Swiss-Prot	strong database homology
`A2X1A1`	Oryza sativa subsp. indica	Auxin response factor 6	55.483%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card