LXL04_012673 | RubberDandelionOmics

Gene overview

LXL04_012673

Reference: OH-1004 Chr: Chr03 Coordinates: 16659292-16665792 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2847 bp · LXL04_012673|LXL04_012673|OH1004|cDNA

ATGCTAGATTGTCGAAGTGGAGAATGGAAGCTACTTTCTATTGGAGGTCGGCTTACGTTACTTAAATCGGTCCTCGGTAGTCTTGGTACGTATTATTTTTCGATGTTCAAAACTCCTAATGCCGTGGGAAAAAGAATGGAATCATGTTGGGCGAAATTCTTTTGGGGTATTGAAGAAAATGAGAGGAAAATTCATTGGACCAAGTGGGATTTAGTTCTTAATGATTTGGAGCATGGTGGTCTCGTAGTGGGTAGCTTGCA...

CDS

Download CDS FASTA

2847 bp · LXL04_012673|LXL04_012673|OH1004|CDS

ATGCTAGATTGTCGAAGTGGAGAATGGAAGCTACTTTCTATTGGAGGTCGGCTTACGTTACTTAAATCGGTCCTCGGTAGTCTTGGTACGTATTATTTTTCGATGTTCAAAACTCCTAATGCCGTGGGAAAAAGAATGGAATCATGTTGGGCGAAATTCTTTTGGGGTATTGAAGAAAATGAGAGGAAAATTCATTGGACCAAGTGGGATTTAGTTCTTAATGATTTGGAGCATGGTGGTCTCGTAGTGGGTAGCTTGCA...

Protein

Download Protein FASTA

948 aa · LXL04_012673|LXL04_012673|OH1004|PROTEIN

MLDCRSGEWKLLSIGGRLTLLKSVLGSLGTYYFSMFKTPNAVGKRMESCWAKFFWGIEENERKIHWTKWDLVLNDLEHGGLVVGSLHALNQALLYKWRWRFLSETEGLISCHGVNGGFPESLGSNHGGVWRGIIANVACLHISGIIPLNVIRRLATVFSRLYRFASNMHAKVADYRGEDGWQFQWRVPIRGGVIQEHIKHLHLQVEHIYIIGGWADSWRWDHKRLPTRWALSNRGITIDKIMCTLCDAVPEQVNHLSFSC...

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_012673`
TK1151 ID	TkA02G546200
OH-1004 ID	LXL04_012673
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.600
Protein coverage (%)	TK1151 89.037 / OH-1004 35.127 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_012673

Location Chr03:16659292-16665792 (-)

Description Similar to LOG2: Probable E3 ubiquitin-protein ligase LOG2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g09770`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates (in vitro).	No verified direct reference in this release
`At5g03200`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates (in vitro).	No verified direct reference in this release
`At3g53410`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates (in vitro).	No verified direct reference in this release
`At5g19080`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates (in vitro).	No verified direct reference in this release
`At3g06140`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates (in vitro).	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_012673 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009737 response to abscisic acid Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0080144 intracellular amino acid homeostasis Biological Process

GO:0090333 regulation of stomatal closure Biological Process

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT3G06140

ath:AT3G09770

ath:AT3G53410

ath:AT5G03200

ath:AT5G19080

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.

Cytoplasm0.514

Rank 1 · LXL04_012673 · OH-1004

Nucleus0.394

Rank 2 · LXL04_012673 · OH-1004

Cell membrane0.125

Rank 3 · LXL04_012673 · OH-1004

Endoplasmic reticulum0.082

Rank 4 · LXL04_012673 · OH-1004

Golgi apparatus0.051

Rank 5 · LXL04_012673 · 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.

PF13966.12zf-RVT218-267 aa

PF26192.1RNF157-like_N467-620 aa

PF13920.13zf-C3HC4_3642-666 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012673	`PF13966.12`	zf-RVT	218	267	3.6e-07	31.4
LXL04_012673	`PF26192.1`	RNF157-like_N	467	620	2.3e-66	223.7
LXL04_012673	`PF13920.13`	zf-C3HC4_3	642	666	8.3e-07	29.4

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
`Q9S752`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase LOG2	66.094%	Swiss-Prot	weak database homology
`Q9LYW5`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase LUL1	54.062%	Swiss-Prot	weak database homology
`Q9LFH6`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase LUL2	59.846%	Swiss-Prot	weak database homology
`Q84ME1`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase LUL3	45.985%	Swiss-Prot	weak database homology
`Q8LA32`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase LUL4	40.840%	Swiss-Prot	weak database homology

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