LXL04_002289 | RubberDandelionOmics

Gene overview

LXL04_002289

Reference: OH-1004 Chr: Chr01 Coordinates: 45344848-45349155 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3111 bp · LXL04_002289|LXL04_002289|OH1004|cDNA

ATGAAAGCTCCGTCAAATGGATATCAACCTAGTTCCGGCGAAGGTACACGGAAGATGATGAACTCAGAGTTATGGCACGCGTGTGCCGGCCCCTTAGTCTCTTTACCTCCTATAGGAAGCCTCGTGGTCTACTTTCCACAAGGTCACAGCGAGCAAGTCGCCGCATCCATGAAGAAAGATACAGAAAACATCCCAAGTTACCCCAATCTTCCCTCCAAACTCATCTGCATGCTTCATAATGTCGCATTACATGCTGATGC...

CDS

Download CDS FASTA

3111 bp · LXL04_002289|LXL04_002289|OH1004|CDS

ATGAAAGCTCCGTCAAATGGATATCAACCTAGTTCCGGCGAAGGTACACGGAAGATGATGAACTCAGAGTTATGGCACGCGTGTGCCGGCCCCTTAGTCTCTTTACCTCCTATAGGAAGCCTCGTGGTCTACTTTCCACAAGGTCACAGCGAGCAAGTCGCCGCATCCATGAAGAAAGATACAGAAAACATCCCAAGTTACCCCAATCTTCCCTCCAAACTCATCTGCATGCTTCATAATGTCGCATTACATGCTGATGC...

Protein

Download Protein FASTA

1036 aa · LXL04_002289|LXL04_002289|OH1004|PROTEIN

MKAPSNGYQPSSGEGTRKMMNSELWHACAGPLVSLPPIGSLVVYFPQGHSEQVAASMKKDTENIPSYPNLPSKLICMLHNVALHADAETDEVYAQMTLQPVTKYDQEALLMSEMGLKQNKQPAEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFSMQPPAQELVARDLHDQSWTFRHIYRGQPKRHLLTTGWSVFVSSKRLSAGDAVLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAATNNR...

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_002289`
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_002289

Location Chr01:45344848-45349155 (+)

Description Similar to ARF19: Auxin response factor 19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g19220`	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).	A role for auxin response factor 19 in auxin and ethylene signaling in Arabidopsis.2006 · DOI: 10.1104/pp.105.070987 ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.047761 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.2017 · DOI: 10.1126/scisignal.aan0316
`At5g20730`	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).	Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4.2004 · DOI: 10.1242/dev.00925 A gradient of auxin and auxin-dependent transcription precedes tropic growth responses.2006 · DOI: 10.1073/pnas.0507127103 A role for auxin response factor 19 in auxin and ethylene signaling in Arabidopsis.2006 · DOI: 10.1104/pp.105.070987 ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.047761 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.2017 · DOI: 10.1126/scisignal.aan0316

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0196700`	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: A2YAA5`	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
`Os02g0141100`	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_002289 · 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:0009630 gravitropism Biological Process

GO:0009638 phototropism Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009785 blue light signaling pathway Biological Process

GO:0010311 lateral root formation Biological Process

GO:0040008 regulation of growth Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0048366 leaf development Biological Process

KEGG gene cross-reference

ath:AT1G19220

ath:AT5G20730

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.

Nucleus0.954

Rank 1 · LXL04_002289 · OH-1004

Cytoplasm0.103

Rank 2 · LXL04_002289 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_002289 · OH-1004

Endoplasmic reticulum0.022

Rank 4 · LXL04_002289 · OH-1004

Plastid0.016

Rank 5 · LXL04_002289 · 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.

PF02362.27B3126-227 aa

PF06507.20ARF_AD275-357 aa

PF02309.23AUX_IAA904-996 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002289	`PF02362.27`	B3	126	227	4.1e-23	81.9
LXL04_002289	`PF06507.20`	ARF_AD	275	357	4.4e-36	123.3
LXL04_002289	`PF02309.23`	AUX_IAA	904	996	6.2e-10	39.9

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
`Q8RYC8`	Arabidopsis thaliana	Auxin response factor 19	75.547%	Swiss-Prot	weak database homology
`P93022`	Arabidopsis thaliana	Auxin response factor 7	77.526%	Swiss-Prot	weak database homology
`A3B9A0`	Oryza sativa subsp. japonica	Auxin response factor 16	77.186%	Swiss-Prot	weak database homology
`A2YAA5`	Oryza sativa subsp. indica	Auxin response factor 16	76.972%	Swiss-Prot	weak database homology
`Q6Z2W3`	Oryza sativa subsp. japonica	Auxin response factor 5	75.181%	Swiss-Prot	weak database homology

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