LXL04_004461 | RubberDandelionOmics

Gene overview

LXL04_004461

Reference: OH-1004 Chr: Chr01 Coordinates: 136734851-136738821 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2273 bp · LXL04_004461|LXL04_004461|OH1004|cDNA

ATGGAAATTGATCTGAACCATGCAGCGAATGGGATTGAGGTTATGGAGAAGCTTTATAGCGTTGATTCGAGTGGAAATGGAGGGGATTCGTCTTTATCAGCTTCGTCAAACTCCTCGAATTCGTCTCTAAAACAATCAAATCCCAATTTTGAATCATCGGTTTATATGGAGCTTTGGCATGCCTGTGCTGGGCCTCTCACAACTCTCCCAAATAAAGgaaatgtggttgtttatttcCCACAAGGTCACTTAGAACAAAC...

CDS

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2265 bp · LXL04_004461|LXL04_004461|OH1004|CDS

ATGGAAATTGATCTGAACCATGCAGCGAATGGGATTGAGGTTATGGAGAAGCTTTATAGCGTTGATTCGAGTGGAAATGGAGGGGATTCGTCTTTATCAGCTTCGTCAAACTCCTCGAATTCGTCTCTAAAACAATCAAATCCCAATTTTGAATCATCGGTTTATATGGAGCTTTGGCATGCCTGTGCTGGGCCTCTCACAACTCTCCCAAATAAAGGAAATGTGGTTGTTTATTTCCCACAAGGTCACTTAGAACAAAC...

Protein

Download Protein FASTA

754 aa · LXL04_004461|LXL04_004461|OH1004|PROTEIN

MEIDLNHAANGIEVMEKLYSVDSSGNGGDSSLSASSNSSNSSLKQSNPNFESSVYMELWHACAGPLTTLPNKGNVVVYFPQGHLEQTASHSSIHFSPMEVPSFGLQPQIFCKVIDVKLLANKENDEIYTKLTLLPLPELTDKNLQEGEEEGGGGTLTKSTPQMFCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYKQQRPSQELVAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFLRGEGGELWL...

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_004461`
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_004461

Location Chr01:136734851-136738821 (-)

Description Similar to ARF4: Auxin response factor 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60450`	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
`At2g33860`	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
`Os05g0563400`	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
`Os01g0670800`	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
`Os01g0753500`	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_004461 · 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:0009850 auxin metabolic process Biological Process

GO:0010050 vegetative phase change Biological Process

GO:0010158 abaxial cell fate specification Biological Process

GO:0010582 floral meristem determinacy Biological Process

GO:1902584 positive regulation of response to water deprivation Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G33860

ath:AT5G60450

dosa:Os01g0670800

dosa:Os01g0753500

dosa:Os05g0563400

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.

Nucleus0.971

Rank 1 · LXL04_004461 · OH-1004

Cytoplasm0.082

Rank 2 · LXL04_004461 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_004461 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_004461 · OH-1004

Plastid0.013

Rank 5 · LXL04_004461 · 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.

PF02362.27B3164-265 aa

PF25313.2BRWD_AD292-393 aa

PF06507.20ARF_AD313-394 aa

PF02309.23AUX_IAA636-722 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004461	`PF02362.27`	B3	164	265	1.9e-23	83.0
LXL04_004461	`PF25313.2`	BRWD_AD	292	393	5.7e-11	43.4
LXL04_004461	`PF06507.20`	ARF_AD	313	394	1e-31	109.4
LXL04_004461	`PF02309.23`	AUX_IAA	636	722	1.4e-10	42.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9ZTX9`	Arabidopsis thaliana	Auxin response factor 4	55.418%	Swiss-Prot	strong database homology
`O23661`	Arabidopsis thaliana	Auxin response factor 3	50.732%	Swiss-Prot	moderate database homology
`Q8S985`	Oryza sativa subsp. japonica	Auxin response factor 15	47.656%	Swiss-Prot	moderate database homology
`Q0JKI9`	Oryza sativa subsp. japonica	Auxin response factor 2	46.708%	Swiss-Prot	moderate database homology
`Q5JMM1`	Oryza sativa subsp. japonica	Auxin response factor 3	44.559%	Swiss-Prot	moderate database homology

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