LXL04_013591 | RubberDandelionOmics

Gene overview

LXL04_013591

Reference: OH-1004 Chr: Chr03 Coordinates: 32197429-32199899 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2232 bp · LXL04_013591|LXL04_013591|OH1004|cDNA

atgAACGATTGGTTATTTCATTACACAGGTGTGATGGAGATATCACTACTGAAAACACTTCTAAAAAACATTTCTAGTTTTCTTCATTTGTCACGCATCGATAATGGATGCAGTGAAATTGTTAAAAAGTACTACATCACCATTGAAGAACTACTGAAGTTAATTAAGCCAGAACTCGAGTCTATTATCGATACAGAACTGGCTTCAGATGAACCACTACAGAAGGAACTTGCAGGCATGAGTCAATCCGTTGATGAACT...

CDS

Download CDS FASTA

2232 bp · LXL04_013591|LXL04_013591|OH1004|CDS

ATGAACGATTGGTTATTTCATTACACAGGTGTGATGGAGATATCACTACTGAAAACACTTCTAAAAAACATTTCTAGTTTTCTTCATTTGTCACGCATCGATAATGGATGCAGTGAAATTGTTAAAAAGTACTACATCACCATTGAAGAACTACTGAAGTTAATTAAGCCAGAACTCGAGTCTATTATCGATACAGAACTGGCTTCAGATGAACCACTACAGAAGGAACTTGCAGGCATGAGTCAATCCGTTGATGAACT...

Protein

Download Protein FASTA

743 aa · LXL04_013591|LXL04_013591|OH1004|PROTEIN

MNDWLFHYTGVMEISLLKTLLKNISSFLHLSRIDNGCSEIVKKYYITIEELLKLIKPELESIIDTELASDEPLQKELAGMSQSVDELKELFEDCHPLMSKVYFVLKVESLLTKVQTHCLEIFEVLQSSCEQLPVELNPSSLEKIKHMGYEKPSDIVSKAIREQVEGSDPTSETRSKIADLLSLKTNQELLIEAVALENLKENAEQAEKSDDLEDIEEMISLITHMHDCYVEMKQSESSNPVPIPPDFCCPLSLQLMTDPV...

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_013591`
TK1151 ID	TkA02G486590
OH-1004 ID	LXL04_013591
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	96.000
Protein coverage (%)	TK1151 94.292 / OH-1004 60.162 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013591

Location Chr03:32197429-32199899 (+)

Description Similar to PUB2: U-box domain-containing protein 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g67340`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At2g23140`	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
`At3g46510`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0102700`	Possesses E3 ubiquitin-protein ligase in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013591 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT2G23140

ath:AT3G46510

ath:AT3G54790

ath:AT5G67340

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.507

Rank 1 · LXL04_013591 · OH-1004

Nucleus0.315

Rank 2 · LXL04_013591 · OH-1004

Cell membrane0.246

Rank 3 · LXL04_013591 · OH-1004

Golgi apparatus0.075

Rank 4 · LXL04_013591 · OH-1004

Endoplasmic reticulum0.065

Rank 5 · LXL04_013591 · 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.

PF25240.2PUB2_N13-144 aa

PF04564.22U-box243-313 aa

PF25598.2ARM_PUB460-735 aa

PF24768.2ARM_ARMC5460-632 aa

PF00514.30Arm491-528 aa

PF00514.30Arm531-569 aa

PF00514.30Arm573-610 aa

PF24768.2ARM_ARMC5604-730 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013591	`PF25240.2`	PUB2_N	13	144	1.9e-49	167.9
LXL04_013591	`PF04564.22`	U-box	243	313	3.2e-20	72.8
LXL04_013591	`PF25598.2`	ARM_PUB	460	735	8.2e-26	91.8
LXL04_013591	`PF24768.2`	ARM_ARMC5	460	632	5.8e-16	59.4
LXL04_013591	`PF00514.30`	Arm	491	528	1.2e-37	127.4
LXL04_013591	`PF00514.30`	Arm	531	569	1.2e-37	127.4
LXL04_013591	`PF00514.30`	Arm	573	610	1.2e-37	127.4
LXL04_013591	`PF24768.2`	ARM_ARMC5	604	730	5.8e-16	59.4

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
`Q5XEZ8`	Arabidopsis thaliana	U-box domain-containing protein 2	48.916%	Swiss-Prot	moderate database homology
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	43.929%	Swiss-Prot	moderate database homology
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	59.202%	Swiss-Prot	weak database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	50.169%	Swiss-Prot	weak database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	52.768%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card