LXL04_013423 | RubberDandelionOmics

Gene overview

LXL04_013423

Reference: OH-1004 Chr: Chr03 Coordinates: 29370607-29371541 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

717 bp · LXL04_013423|LXL04_013423|OH1004|cDNA

ATGGGTTCCGTTTGTTGCTGCTTGCGTGATGAATGTGAAGATTACGTTAATCCCAATAGTTCCGTATACAGAAATTGCATATGTCTCCGTTGCTTCCTTCAAAATTTCTTATATATGTACACATCGTTATTCCAAAGAGGTGAAGAACACGTGAGGCTTCCAATTAGCCCTAACTCCATCCAAGGGACAACAACTTCCTTCAGTTCATCAGCATCACTCGACAACTCTCTATCTGGGGTGTACAGATCACCCCCTAGACC...

CDS

Download CDS FASTA

717 bp · LXL04_013423|LXL04_013423|OH1004|CDS

ATGGGTTCCGTTTGTTGCTGCTTGCGTGATGAATGTGAAGATTACGTTAATCCCAATAGTTCCGTATACAGAAATTGCATATGTCTCCGTTGCTTCCTTCAAAATTTCTTATATATGTACACATCGTTATTCCAAAGAGGTGAAGAACACGTGAGGCTTCCAATTAGCCCTAACTCCATCCAAGGGACAACAACTTCCTTCAGTTCATCAGCATCACTCGACAACTCTCTATCTGGGGTGTACAGATCACCCCCTAGACC...

Protein

Download Protein FASTA

238 aa · LXL04_013423|LXL04_013423|OH1004|PROTEIN

MGSVCCCLRDECEDYVNPNSSVYRNCICLRCFLQNFLYMYTSLFQRGEEHVRLPISPNSIQGTTTSFSSSASLDNSLSGVYRSPPRPLPYDVDPRYTRLQRDGLVSRREKGSSRSQEEEGEPLRGSDSDTETDPLCSGSKWNNNNSSTCEDGTTTKGLQTKSSFKVSSMRESTGFAHIFTSSEDEDVCPTCLEEYTTENPKIVTKCSHHFHLGCIYEWMERSESCPVCGKVMAFEETI

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_013423`
TK1151 ID	TkA02G497150
OH-1004 ID	LXL04_013423
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.000
Protein coverage (%)	TK1151 91.011 / OH-1004 73.109 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_013423

Location Chr03:29370607-29371541 (+)

Description Similar to At3g02290: E3 ubiquitin-protein ligase At3g02290

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02290`	Mediates E2-dependent protein ubiquitination.	No verified direct reference in this release
`At4g23450`	Possesses E3 ubiquitin-protein ligase activity in vitro when associated with the E2 enzyme UBC8 in vitro.	The Arabidopsis C3H2C3-type RING E3 ubiquitin ligase AtAIRP1 is a positive regulator of an abscisic acid-dependent response to drought stress.2010 · DOI: 10.1104/pp.110.164749
`At4g00335`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At4g14220`	E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression.	Targeted degradation of the cyclin-dependent kinase inhibitor ICK4/KRP6 by RING-type E3 ligases is essential for mitotic cell cycle progression during Arabidopsis gametogenesis.2008 · DOI: 10.1105/tpc.108.059741
`At5g22000`	E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression.	Targeted degradation of the cyclin-dependent kinase inhibitor ICK4/KRP6 by RING-type E3 ligases is essential for mitotic cell cycle progression during Arabidopsis gametogenesis.2008 · DOI: 10.1105/tpc.108.059741

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013423 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009414 response to water deprivation Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010498 proteasomal protein catabolic process Biological Process

GO:0010729 positive regulation of hydrogen peroxide biosynthetic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051603 proteolysis involved in protein catabolic process Biological Process

GO:0051726 regulation of cell cycle Biological Process

GO:0055046 microgametogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT3G02290

ath:AT4G00335

ath:AT4G14220

ath:AT4G23450

ath:AT5G22000

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.

Cytoplasm0.277

Rank 1 · LXL04_013423 · OH-1004

Cell membrane0.277

Rank 2 · LXL04_013423 · OH-1004

Nucleus0.262

Rank 3 · LXL04_013423 · OH-1004

Endoplasmic reticulum0.158

Rank 4 · LXL04_013423 · OH-1004

Lysosome / Vacuole0.157

Rank 5 · LXL04_013423 · 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.

PF12678.14zf-rbx1185-228 aa

PF12861.14zf-ANAPC11186-235 aa

PF13639.13zf-RING_2187-228 aa

PF13923.13zf-C3HC4_2188-228 aa

PF00097.32zf-C3HC4188-228 aa

PF13445.13zf-RING_UBOX188-226 aa

PF14634.13zf-RING_5188-230 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013423	`PF12678.14`	zf-rbx1	185	228	2.8e-11	44.2
LXL04_013423	`PF12861.14`	zf-ANAPC11	186	235	1.4e-07	32.2
LXL04_013423	`PF13639.13`	zf-RING_2	187	228	6.3e-12	46.3
LXL04_013423	`PF13923.13`	zf-C3HC4_2	188	228	3.5e-08	33.8
LXL04_013423	`PF00097.32`	zf-C3HC4	188	228	1.1e-06	29.1
LXL04_013423	`PF13445.13`	zf-RING_UBOX	188	226	3.5e-06	27.6
LXL04_013423	`PF14634.13`	zf-RING_5	188	230	5.8e-06	26.9

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
`Q8LE94`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At3g02290	57.025%	Swiss-Prot	strong database homology
`Q93ZF6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase AIRP1	44.211%	Swiss-Prot	weak database homology
`Q2HIJ8`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHB1A	30.899%	Swiss-Prot	moderate database homology
`Q4TU14`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHF1A	39.062%	Swiss-Prot	weak database homology
`Q9ZT42`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHF2A	38.462%	Swiss-Prot	weak database homology

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