LXL04_032513 | RubberDandelionOmics

Gene overview

LXL04_032513

Reference: OH-1004 Chr: Chr07 Coordinates: 24390322-24395450 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1284 bp · LXL04_032513|LXL04_032513|OH1004|cDNA

ATGAACAATTCAAGAGAATTACAAGGTAAAATGGCTCATGATCCTGGCTGTGTGTTTTCTTACCCAAAAAGGAGACGTCAAGTATGGGTTCCTGGTCCAGTCATAGTCGGAGCCGGACCATCTGGCCTCGCCGCTGCTGCCTGCTTGAGGGAGAAAGGAGTTCCTAGCGTCATCCTCGAACGATCAAATTGCATAGCGTCCCTTTGGCAGCTCAAAACCTACGACCGCCTCCGGCTACACCTTCCAAAAAAGTTCTGTGA...

CDS

Download CDS FASTA

1284 bp · LXL04_032513|LXL04_032513|OH1004|CDS

ATGAACAATTCAAGAGAATTACAAGGTAAAATGGCTCATGATCCTGGCTGTGTGTTTTCTTACCCAAAAAGGAGACGTCAAGTATGGGTTCCTGGTCCAGTCATAGTCGGAGCCGGACCATCTGGCCTCGCCGCTGCTGCCTGCTTGAGGGAGAAAGGAGTTCCTAGCGTCATCCTCGAACGATCAAATTGCATAGCGTCCCTTTGGCAGCTCAAAACCTACGACCGCCTCCGGCTACACCTTCCAAAAAAGTTCTGTGA...

Protein

Download Protein FASTA

427 aa · LXL04_032513|LXL04_032513|OH1004|PROTEIN

MNNSRELQGKMAHDPGCVFSYPKRRRQVWVPGPVIVGAGPSGLAAAACLREKGVPSVILERSNCIASLWQLKTYDRLRLHLPKKFCELPLLSFPEDFPTYPTKQQFIEYLETYAKRFGIEPVFEQSVESAEYDESVEMWRVRSVGMKGEEMEYVCRWLVVATGENAEAVLPNIKGMAEFCGEVKHTSEYKSGSAYKGKKVLVVGCGNSGMEVCLDLCNHNAKPSLVVRDAVHVLPRDIMGQSTFGLSMRLLKWLPMRLVD...

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_032513`
TK1151 ID	TkA08G183020
OH-1004 ID	LXL04_032513
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_032513

Location Chr07:24390322-24395450 (-)

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
`At5g43890`	Involved in auxin biosynthesis.	Interaction of auxin and ERECTA in elaborating Arabidopsis inflorescence architecture revealed by the activation tagging of a new member of the YUCCA family putative flavin monooxygenases.2005 · DOI: 10.1104/pp.105.063495
`At4g28720`	Involved in auxin biosynthesis.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032513 · 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:0009735 response to cytokinin Biological Process

GO:0009742 brassinosteroid mediated signaling pathway 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:0010600 regulation of auxin biosynthetic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G04180

ath:AT4G13260

ath:AT4G28720

ath:AT5G25620

ath:AT5G43890

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.

Cytoplasm0.343

Rank 1 · LXL04_032513 · OH-1004

Endoplasmic reticulum0.205

Rank 2 · LXL04_032513 · OH-1004

Nucleus0.163

Rank 3 · LXL04_032513 · OH-1004

Mitochondrion0.155

Rank 4 · LXL04_032513 · OH-1004

Cell membrane0.099

Rank 5 · LXL04_032513 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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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_234-227 aa

PF01494.26FAD_binding_334-63 aa

PF00743.26FMO-like35-355 aa

PF13434.13Lys_Orn_oxgnase99-225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032513	`PF13738.13`	Pyr_redox_3	34	230	2.7e-27	96.6
LXL04_032513	`PF07992.21`	Pyr_redox_2	34	227	7.3e-16	59.2
LXL04_032513	`PF01494.26`	FAD_binding_3	34	63	2.2e-08	34.4
LXL04_032513	`PF00743.26`	FMO-like	35	355	2.3e-27	96.4
LXL04_032513	`PF13434.13`	Lys_Orn_oxgnase	99	225	5.1e-17	62.7

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
`Q8VZ59`	Arabidopsis thaliana	Indole-3-pyruvate monooxygenase YUCCA6	70.516%	Swiss-Prot	strong database homology
`Q9SVQ1`	Arabidopsis thaliana	Indole-3-pyruvate monooxygenase YUCCA2	64.444%	Swiss-Prot	strong database homology
`O64489`	Arabidopsis thaliana	Probable indole-3-pyruvate monooxygenase YUCCA9	63.613%	Swiss-Prot	strong database homology
`Q9LKC0`	Arabidopsis thaliana	Probable indole-3-pyruvate monooxygenase YUCCA5	62.500%	Swiss-Prot	strong database homology
`Q9SVU0`	Arabidopsis thaliana	Probable indole-3-pyruvate monooxygenase YUCCA8	58.809%	Swiss-Prot	strong database homology

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