LXL04_009555 | RubberDandelionOmics

Gene overview

LXL04_009555

Reference: OH-1004 Chr: Chr02 Coordinates: 128933101-128934926 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1038 bp · LXL04_009555|LXL04_009555|OH1004|cDNA

ATGACCATCAAAGGCGCAGATTTTAAGTGGTACGATGGGTTTTTCCTATCGATGCTTGCCACTAGCATAATAATCATAGCGATCAATTGGAACCATTACCATCTCTGCACTCACCCATTGCACATATGGATTGTGGTCGACTACTCAACAGTTTTCGTGTTCCGTCTCTTGATGTTTGTGGACAATGGACTCGCTGCAGGAATGGGATTGGATTTTGGCCGACAACAAAGGCACGCTCGTTTTTGTGGAAGAGTTGCAGT...

CDS

Download CDS FASTA

1038 bp · LXL04_009555|LXL04_009555|OH1004|CDS

ATGACCATCAAAGGCGCAGATTTTAAGTGGTACGATGGGTTTTTCCTATCGATGCTTGCCACTAGCATAATAATCATAGCGATCAATTGGAACCATTACCATCTCTGCACTCACCCATTGCACATATGGATTGTGGTCGACTACTCAACAGTTTTCGTGTTCCGTCTCTTGATGTTTGTGGACAATGGACTCGCTGCAGGAATGGGATTGGATTTTGGCCGACAACAAAGGCACGCTCGTTTTTGTGGAAGAGTTGCAGT...

Protein

Download Protein FASTA

345 aa · LXL04_009555|LXL04_009555|OH1004|PROTEIN

MTIKGADFKWYDGFFLSMLATSIIIIAINWNHYHLCTHPLHIWIVVDYSTVFVFRLLMFVDNGLAAGMGLDFGRQQRHARFCGRVAVLSILCVLLYPFLWAWTIIGSLWFSSARDCLPEEGQKWGFLIWLLFSYCGLICLAGMSMKTWLRRRQAHALRAQQGIPLSEYGVLVDMIRVPDFAFESAAGQELRGMGQDAASYHPGLYLTEPQREAVEALIQELPKFMLKAVPTDCSECPICLEEFHVGNEVRGLPCAHNFHV...

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_009555`
TK1151 ID	TkA03G448300
OH-1004 ID	LXL04_009555
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.400
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

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_009555

Location Chr02:128933101-128934926 (-)

Description Similar to SIS3: E3 ubiquitin-protein ligase SIS3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g47990`	E3 ubiquitin protein ligase that acts as a positive regulator of sugar signaling during early seedling development.	SUGAR-INSENSITIVE3, a RING E3 ligase, is a new player in plant sugar response.2010 · DOI: 10.1104/pp.109.150573
`At5g66070`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At4g11680`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At2g17730`	Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.	No verified direct reference in this release
`At1g22500`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, UBC28 and UBC29 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_009555 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006952 defense response Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010182 sugar mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0033591 response to L-ascorbic acid Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT1G22500

ath:AT2G17730

ath:AT3G47990

ath:AT4G11680

ath:AT5G66070

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.

Golgi apparatus0.287

Rank 1 · LXL04_009555 · OH-1004

Cytoplasm0.277

Rank 2 · LXL04_009555 · OH-1004

Endoplasmic reticulum0.251

Rank 3 · LXL04_009555 · OH-1004

Cell membrane0.225

Rank 4 · LXL04_009555 · OH-1004

Lysosome / Vacuole0.215

Rank 5 · LXL04_009555 · 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.

PF26753.1SIS3_N11-161 aa

PF13639.13zf-RING_2235-277 aa

PF17123.12zf-RING_11235-263 aa

PF13923.13zf-C3HC4_2235-276 aa

PF00097.32zf-C3HC4236-276 aa

PF13445.13zf-RING_UBOX236-274 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009555	`PF26753.1`	SIS3_N	11	161	6.2e-70	234.6
LXL04_009555	`PF13639.13`	zf-RING_2	235	277	1.7e-14	54.5
LXL04_009555	`PF17123.12`	zf-RING_11	235	263	1.7e-09	37.9
LXL04_009555	`PF13923.13`	zf-C3HC4_2	235	276	1.9e-08	34.7
LXL04_009555	`PF00097.32`	zf-C3HC4	236	276	6e-08	33.1
LXL04_009555	`PF13445.13`	zf-RING_UBOX	236	274	8.6e-08	32.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8GYT9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SIS3	68.927%	Swiss-Prot	strong database homology
`Q9FKX5`	Arabidopsis thaliana	NEP1-interacting protein-like 1	32.979%	Swiss-Prot	weak database homology
`Q93Z92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At4g11680	25.728%	Swiss-Prot	weak database homology
`Q8GT74`	Arabidopsis thaliana	NEP1-interacting protein 2	35.294%	Swiss-Prot	weak database homology
`Q9SK92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL15	41.463%	Swiss-Prot	weak database homology

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