LXL04_030338 | RubberDandelionOmics

Gene overview

LXL04_030338

Reference: OH-1004 Chr: Chr06 Coordinates: 114507156-114508914 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1203 bp · LXL04_030338|LXL04_030338|OH1004|cDNA

ATGGTTGTCCACGTGTCACCTCTTACCCAACTCCTTCCTCCAGGTGTTCCCcttcttctttccttttctATATCAACACCATCAAAATTCAAGACCAAATTCCCTACACGTTTGTTTCTCTCTTTCTCAATCACCCCCCGGAAATCCATGGAGACGGAAATACAGGCGAATTACTCATACATGGGACGGAATTTCAGCAACATCAGCCTCACCAACGATCACTCCGCGGCGTTCAGCGATTGTAATAGCGACCGGTCAGG...

CDS

Download CDS FASTA

1203 bp · LXL04_030338|LXL04_030338|OH1004|CDS

ATGGTTGTCCACGTGTCACCTCTTACCCAACTCCTTCCTCCAGGTGTTCCCCTTCTTCTTTCCTTTTCTATATCAACACCATCAAAATTCAAGACCAAATTCCCTACACGTTTGTTTCTCTCTTTCTCAATCACCCCCCGGAAATCCATGGAGACGGAAATACAGGCGAATTACTCATACATGGGACGGAATTTCAGCAACATCAGCCTCACCAACGATCACTCCGCGGCGTTCAGCGATTGTAATAGCGACCGGTCAGG...

Protein

Download Protein FASTA

400 aa · LXL04_030338|LXL04_030338|OH1004|PROTEIN

MVVHVSPLTQLLPPGVPLLLSFSISTPSKFKTKFPTRLFLSFSITPRKSMETEIQANYSYMGRNFSNISLTNDHSAAFSDCNSDRSGEFPTTSASKRLLLACATESSDDLIKQLVSDLDSDSIEDQKQAAMELRLLAKNKPENRVKIARAGAIRPLISLISSADSELQEHGVTAILNLSLCDENKEVLASSGAIRPLVRALKVGTPTAKENAACALLRLSQLEENKAAIGRSGAIPLLVDLLETGNFRGQKDASTALYSL...

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_030338`
TK1151 ID	TkA07G398260
OH-1004 ID	LXL04_030338
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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_030338

Location Chr06:114507156-114508914 (+)

Description Similar to PUB4: U-box domain-containing protein 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g23140`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g67340`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g54790`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g23030`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g71020`	Functions as an E3 ubiquitin ligase.	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_030338 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0031648 protein destabilization Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0090333 regulation of stomatal closure Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:2000022 regulation of jasmonic acid mediated signaling pathway Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

KEGG gene cross-reference

ath:AT1G23030

ath:AT1G71020

ath:AT2G23140

ath:AT3G54790

ath:AT5G67340

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.

Cytoplasm0.344

Rank 1 · LXL04_030338 · OH-1004

Nucleus0.311

Rank 2 · LXL04_030338 · OH-1004

Plastid0.255

Rank 3 · LXL04_030338 · OH-1004

Cell membrane0.107

Rank 4 · LXL04_030338 · OH-1004

Mitochondrion0.051

Rank 5 · LXL04_030338 · 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.

PF24768.2ARM_ARMC5108-293 aa

PF25598.2ARM_PUB113-386 aa

PF00514.30Arm141-179 aa

PF00514.30Arm182-220 aa

PF00514.30Arm224-262 aa

PF28415.2SIL1_FES1_HPBP1_C231-351 aa

PF24768.2ARM_ARMC5256-375 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030338	`PF24768.2`	ARM_ARMC5	108	293	2e-18	67.5
LXL04_030338	`PF25598.2`	ARM_PUB	113	386	1.3e-21	78.0
LXL04_030338	`PF00514.30`	Arm	141	179	1.8e-36	123.7
LXL04_030338	`PF00514.30`	Arm	182	220	1.8e-36	123.7
LXL04_030338	`PF00514.30`	Arm	224	262	1.8e-36	123.7
LXL04_030338	`PF28415.2`	SIL1_FES1_HPBP1_C	231	351	8e-07	29.5
LXL04_030338	`PF24768.2`	ARM_ARMC5	256	375	2e-18	67.5

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
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	46.970%	Swiss-Prot	moderate database homology
`Q5XEZ8`	Arabidopsis thaliana	U-box domain-containing protein 2	47.872%	Swiss-Prot	moderate database homology
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	43.909%	Swiss-Prot	moderate database homology
`Q8GUG9`	Arabidopsis thaliana	U-box domain-containing protein 11	44.056%	Swiss-Prot	moderate database homology
`Q9C9A6`	Arabidopsis thaliana	U-box domain-containing protein 10	45.324%	Swiss-Prot	moderate database homology

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