LXL04_025866 | RubberDandelionOmics

Gene overview

LXL04_025866

Reference: OH-1004 Chr: Chr05 Coordinates: 117923469-117926065 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1284 bp · LXL04_025866|LXL04_025866|OH1004|cDNA

ATGAGTTGTTTAAGAGAATTGGAAGGCAAAATGGCTCATGATCCTCACTTTAACCAAGGCGTTATTGGTCTCCGGCGCCGTGTATGGGTCCCCGGTCCGGTCATTGTCGGGGCTGGGCCCTCTGGGCTTGCGGCTGCTGCCTGTTTGAAGGATAAAGGGGTGCCGAGCATCATTTTGGAGAGATCGAATTGCATCGCTTCTCTCTGGCAATTCAGGACGTATGATCGGCTCCGGTTGCATCTTCCGAAGAAGTTCTGTGA...

CDS

Download CDS FASTA

1284 bp · LXL04_025866|LXL04_025866|OH1004|CDS

ATGAGTTGTTTAAGAGAATTGGAAGGCAAAATGGCTCATGATCCTCACTTTAACCAAGGCGTTATTGGTCTCCGGCGCCGTGTATGGGTCCCCGGTCCGGTCATTGTCGGGGCTGGGCCCTCTGGGCTTGCGGCTGCTGCCTGTTTGAAGGATAAAGGGGTGCCGAGCATCATTTTGGAGAGATCGAATTGCATCGCTTCTCTCTGGCAATTCAGGACGTATGATCGGCTCCGGTTGCATCTTCCGAAGAAGTTCTGTGA...

Protein

Download Protein FASTA

427 aa · LXL04_025866|LXL04_025866|OH1004|PROTEIN

MSCLRELEGKMAHDPHFNQGVIGLRRRVWVPGPVIVGAGPSGLAAAACLKDKGVPSIILERSNCIASLWQFRTYDRLRLHLPKKFCELPMMPYPEDFPMYPSKQQFVEYLEAYAKRFGIKPVFEQEVESAGYDDSVGLWRVKSVGLKGEETEYVCRWLVVATGENAEAVVPEIKGIENFRGEVQHTAEYRSGSGFRGKKVLVVGCGNSGMEVSLDLCNHDAHPSLVVRNAVHVLPREMLGRSTFGLSMWLLKWLPIRLVD...

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_025866`
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_025866

Location Chr05:117923469-117926065 (+)

Description Similar to YUC6: Indole-3-pyruvate monooxygenase YUCCA6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g25620`	Involved in auxin biosynthesis via the indole-3-pyruvic acid (IPA) pathway.	Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis.2006 · DOI: 10.1101/gad.1415106 yucca6, a dominant mutation in Arabidopsis, affects auxin accumulation and auxin-related phenotypes.2007 · DOI: 10.1104/pp.107.104935 Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit.2013 · DOI: 10.1093/mp/sss100 The biochemical mechanism of auxin biosynthesis by an arabidopsis YUCCA flavin-containing monooxygenase.2013 · DOI: 10.1074/jbc.m112.424077
`At4g13260`	Involved in auxin biosynthesis.	Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis.2006 · DOI: 10.1101/gad.1415106
`At1g04180`	Involved in auxin biosynthesis.	No verified direct reference in this release
`At1g04610`	Involved in auxin biosynthesis.	No verified direct reference in this release
`At5g11320`	Involved in auxin biosynthesis.	Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis.2006 · DOI: 10.1101/gad.1415106 Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis.2007 · DOI: 10.1105/tpc.107.053009

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025866 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006979 response to oxidative stress Biological Process

GO:0009635 response to herbicide Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009819 drought recovery Biological Process

GO:0009851 auxin biosynthetic process Biological Process

GO:0010038 response to metal ion Biological Process

GO:0010262 somatic embryogenesis Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G04180

ath:AT1G04610

ath:AT4G13260

ath:AT5G11320

ath:AT5G25620

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.

Cytoplasm0.317

Rank 1 · LXL04_025866 · OH-1004

Mitochondrion0.191

Rank 2 · LXL04_025866 · OH-1004

Endoplasmic reticulum0.175

Rank 3 · LXL04_025866 · OH-1004

Nucleus0.155

Rank 4 · LXL04_025866 · OH-1004

Cell membrane0.095

Rank 5 · LXL04_025866 · 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.

PF13738.13Pyr_redox_334-230 aa

PF07992.21Pyr_redox_234-229 aa

PF01494.26FAD_binding_334-63 aa

PF00743.26FMO-like35-350 aa

PF13434.13Lys_Orn_oxgnase99-225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025866	`PF13738.13`	Pyr_redox_3	34	230	1.3e-27	97.6
LXL04_025866	`PF07992.21`	Pyr_redox_2	34	229	1.5e-13	51.5
LXL04_025866	`PF01494.26`	FAD_binding_3	34	63	2e-07	31.3
LXL04_025866	`PF00743.26`	FMO-like	35	350	3.3e-32	112.4
LXL04_025866	`PF13434.13`	Lys_Orn_oxgnase	99	225	6.7e-15	55.8

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
`Q8VZ59`	Arabidopsis thaliana	Indole-3-pyruvate monooxygenase YUCCA6	67.883%	Swiss-Prot	strong database homology
`Q9SVQ1`	Arabidopsis thaliana	Indole-3-pyruvate monooxygenase YUCCA2	65.764%	Swiss-Prot	strong database homology
`O64489`	Arabidopsis thaliana	Probable indole-3-pyruvate monooxygenase YUCCA9	62.010%	Swiss-Prot	strong database homology
`O23024`	Arabidopsis thaliana	Probable indole-3-pyruvate monooxygenase YUCCA3	60.302%	Swiss-Prot	strong database homology
`Q9LFM5`	Arabidopsis thaliana	Probable indole-3-pyruvate monooxygenase YUCCA4	60.733%	Swiss-Prot	strong database homology

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