LXL04_012259 | RubberDandelionOmics

Gene overview

LXL04_012259

Reference: OH-1004 Chr: Chr03 Coordinates: 9249853-9252669 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1767 bp · LXL04_012259|LXL04_012259|OH1004|cDNA

ATGGAGGATCGGAACTACTCCGGCCAGTTCCAGCGGTTTCACGGCATGTCCGACATCGTTTTCGAGTGCGTACTATCATACATACACGACACACGTGACCGCCAGTCGATATCGTTGGTCTGCCGGAGGTTATGCGAACTCGAAGCTCATACGCGGAAACACGTAACGATAGCGCTGTGTTATACGGCGACTCCTAAACAGCTCTCACGGCGGTTCCCGTTTCTTGAGTCGTTGAAGATAAAAGGGAAGCCACGCGCCGC...

CDS

Download CDS FASTA

1767 bp · LXL04_012259|LXL04_012259|OH1004|CDS

ATGGAGGATCGGAACTACTCCGGCCAGTTCCAGCGGTTTCACGGCATGTCCGACATCGTTTTCGAGTGCGTACTATCATACATACACGACACACGTGACCGCCAGTCGATATCGTTGGTCTGCCGGAGGTTATGCGAACTCGAAGCTCATACGCGGAAACACGTAACGATAGCGCTGTGTTATACGGCGACTCCTAAACAGCTCTCACGGCGGTTCCCGTTTCTTGAGTCGTTGAAGATAAAAGGGAAGCCACGCGCCGC...

Protein

Download Protein FASTA

588 aa · LXL04_012259|LXL04_012259|OH1004|PROTEIN

MEDRNYSGQFQRFHGMSDIVFECVLSYIHDTRDRQSISLVCRRLCELEAHTRKHVTIALCYTATPKQLSRRFPFLESLKIKGKPRAAMYNLIPEDWGGFATPWVEEIAKSFSCIKAVHFRRMIVKDEDLELLARERGSVLQVLKLDKCSGFSTDGLRHVCRSCRNLKILFLEESQIQENDGDWLHELAINNTGVLEMLNFYMTDLNQVSVKDLELLAKKCSNLISVKIGDCEILDLVSFLNHANSLEEFGGGCFNEQPER...

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_012259`
TK1151 ID	TkA02G577910
OH-1004 ID	LXL04_012259
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
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

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Basic Information and Functional Annotation

Gene ID LXL04_012259

Location Chr03:9249853-9252669 (-)

Description Similar to COI1: Coronatine-insensitive protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g39940`	Required for jasmonate-regulated plant fertility and defense processes, and for coronatine and/or other elicitors perceptions/responses.	Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis.2000 · DOI: 10.1105/tpc.12.5.707 The SCF(COI1) ubiquitin-ligase complexes are required for jasmonate response in Arabidopsis.2002 · DOI: 10.1105/tpc.003368 A conditionally fertile coi1 allele indicates cross-talk between plant hormone signalling pathways in Arabidopsis thaliana seeds and young seedlings.2002 · DOI: 10.1007/s00425-002-0787-4 Arabidopsis Mutants Selected for Resistance to the Phytotoxin Coronatine Are Male Sterile, Insensitive to Methyl Jasmonate, and Resistant to a Bacterial Pathogen.1994 · DOI: 10.1105/tpc.6.5.751 COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase complex in Arabidopsis.2002 · DOI: 10.1046/j.1365-313x.2002.01432.x Characterization of the early response of Arabidopsis to Alternaria brassicicola infection using expression profiling.2003 · DOI: 10.1104/pp.103.022186 Activation of a COI1-dependent pathway in Arabidopsis by Pseudomonas syringae type III effectors and coronatine.2004 · DOI: 10.1111/j.1365-313x.2003.01986.x COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility.1998 · DOI: 10.1126/science.280.5366.1091

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0449500`	Involved in jasmonate (JA) signaling.	Oryza sativa COI homologues restore jasmonate signal transduction in Arabidopsis coi1-1 mutants.2013 · DOI: 10.1371/journal.pone.0052802
`Os01g0853400`	Involved in jasmonate (JA) signaling.	OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice.2011 · DOI: 10.1111/j.1365-313x.2010.04477.x Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade.2012 · DOI: 10.1073/pnas.1201616109 silencing COI1 in rice increases susceptibility to chewing insects and impairs inducible defense.2012 · DOI: 10.1371/journal.pone.0036214 Oryza sativa COI homologues restore jasmonate signal transduction in Arabidopsis coi1-1 mutants.2013 · DOI: 10.1371/journal.pone.0052802 Priming of jasmonate-mediated antiherbivore defense responses in rice by silicon.2013 · DOI: 10.1073/pnas.1305848110
`UniProt: A2WX30`	Involved in jasmonate (JA) signaling.	No verified direct reference in this release
`Os03g0265500`	Involved in jasmonate (JA) signaling.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012259 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002213 defense response to insect Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006952 defense response Biological Process

GO:0009611 response to wounding Biological Process

GO:0009625 response to insect Biological Process

GO:0009641 shade avoidance Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0009861 jasmonic acid and ethylene-dependent systemic resistance Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0009901 anther dehiscence Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010118 stomatal movement Biological Process

KEGG gene cross-reference

ath:AT2G39940

dosa:Os01g0853400

dosa:Os03g0265500

dosa:Os05g0449500

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.

Nucleus0.663

Rank 1 · LXL04_012259 · OH-1004

Cytoplasm0.235

Rank 2 · LXL04_012259 · OH-1004

Plastid0.062

Rank 3 · LXL04_012259 · OH-1004

Cell membrane0.058

Rank 4 · LXL04_012259 · OH-1004

Mitochondrion0.039

Rank 5 · LXL04_012259 · 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.

PF18511.7F-box_515-54 aa

PF18791.8Transp_inhibit74-119 aa

PF29594.1LRR_SKP2105-239 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012259	`PF18511.7`	F-box_5	15	54	4e-16	59.0
LXL04_012259	`PF18791.8`	Transp_inhibit	74	119	8.5e-22	77.1
LXL04_012259	`PF29594.1`	LRR_SKP2	105	239	1.1e-13	51.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O04197`	Arabidopsis thaliana	Coronatine-insensitive protein 1	66.081%	Swiss-Prot	strong database homology
`Q60EH4`	Oryza sativa subsp. japonica	Coronatine-insensitive protein homolog 1b	60.000%	Swiss-Prot	strong database homology
`Q6Y9P5`	Oryza sativa subsp. japonica	Coronatine-insensitive protein homolog 1a	59.233%	Swiss-Prot	strong database homology
`A2WX30`	Oryza sativa subsp. indica	Coronatine-insensitive protein homolog 1a	59.233%	Swiss-Prot	strong database homology
`Q84QA7`	Oryza sativa subsp. japonica	Coronatine-insensitive protein homolog 2	57.465%	Swiss-Prot	strong database homology

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