LXL04_031851 | RubberDandelionOmics

Gene overview

LXL04_031851

Reference: OH-1004 Chr: Chr07 Coordinates: 12211130-12214125 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1296 bp · LXL04_031851|LXL04_031851|OH1004|cDNA

ATGGCGATCAGAGGCGTACACTTCAAGTGGTACGATGGATTCTTTCTAATAATGCTTGCGTTTAGTATAGTTATGGTTCTATTGAGTTGGAGGCGTTACTATCTTTGTAAATTTCCATTGCATCTGTGGATAGTGGTTGATTATAGTGCTGTGTTTGTTTTTCGCCTCTTAATGTTTGTAGATAATGGTCTTGCAGCTGGAATGGGACTGGATTATGGTAGGCGGCAAAGAGATGTTTGTTTTTATGGAAGAGTAGTAGT...

CDS

Download CDS FASTA

1296 bp · LXL04_031851|LXL04_031851|OH1004|CDS

ATGGCGATCAGAGGCGTACACTTCAAGTGGTACGATGGATTCTTTCTAATAATGCTTGCGTTTAGTATAGTTATGGTTCTATTGAGTTGGAGGCGTTACTATCTTTGTAAATTTCCATTGCATCTGTGGATAGTGGTTGATTATAGTGCTGTGTTTGTTTTTCGCCTCTTAATGTTTGTAGATAATGGTCTTGCAGCTGGAATGGGACTGGATTATGGTAGGCGGCAAAGAGATGTTTGTTTTTATGGAAGAGTAGTAGT...

Protein

Download Protein FASTA

431 aa · LXL04_031851|LXL04_031851|OH1004|PROTEIN

MAIRGVHFKWYDGFFLIMLAFSIVMVLLSWRRYYLCKFPLHLWIVVDYSAVFVFRLLMFVDNGLAAGMGLDYGRRQRDVCFYGRVVVLSILYVVLYPFLWAWSVTGSIWFSYAHACLPEKNQKWGFLVWLIFSYCGLVCLAVYSVNKWLRRRKAHFERAQQGIPISGISEYGVLVDMIRLPDWVFESAAQEMRVMENDATPHHPGLYLSDAQRQAVEILVQELPLFSLKAVPTDCSDCPICLEEFHVEDEVRGLPCAHNF...

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_031851`
TK1151 ID	TkA08G132660
OH-1004 ID	LXL04_031851
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 92.365 / OH-1004 87.007 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_031851

Location Chr07:12211130-12214125 (+)

Description Similar to SIS3: E3 ubiquitin-protein ligase SIS3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At5g57750`	Putative RING-H2 finger protein ATL50.	No verified direct reference in this release
`At3g03550`	RING-H2 finger protein ATL51.	No verified direct reference in this release
`At2g18650`	May be involved in female gametophyte development.	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_031851 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010182 sugar mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0043409 negative regulation of MAPK cascade Biological Process

GO:0071466 cellular response to xenobiotic stimulus Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005770 late endosome Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

KEGG gene cross-reference

ath:AT2G18650

ath:AT3G03550

ath:AT3G47990

ath:AT5G57750

mmu:67702

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.

Lysosome / Vacuole0.302

Rank 1 · LXL04_031851 · OH-1004

Endoplasmic reticulum0.268

Rank 2 · LXL04_031851 · OH-1004

Cytoplasm0.223

Rank 3 · LXL04_031851 · OH-1004

Cell membrane0.198

Rank 4 · LXL04_031851 · OH-1004

Golgi apparatus0.197

Rank 5 · LXL04_031851 · 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_2237-279 aa

PF17123.12zf-RING_11237-265 aa

PF13445.13zf-RING_UBOX238-276 aa

PF00097.32zf-C3HC4238-278 aa

PF13923.13zf-C3HC4_2238-278 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031851	`PF26753.1`	SIS3_N	11	161	8.9e-65	217.9
LXL04_031851	`PF13639.13`	zf-RING_2	237	279	2.7e-14	53.9
LXL04_031851	`PF17123.12`	zf-RING_11	237	265	9.4e-10	38.7
LXL04_031851	`PF13445.13`	zf-RING_UBOX	238	276	4.8e-08	33.6
LXL04_031851	`PF00097.32`	zf-C3HC4	238	278	1.3e-07	32.0
LXL04_031851	`PF13923.13`	zf-C3HC4_2	238	278	1.5e-07	31.8

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	60.756%	Swiss-Prot	strong database homology
`Q9FHG8`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL50	51.562%	Swiss-Prot	weak database homology
`Q9SRQ8`	Arabidopsis thaliana	RING-H2 finger protein ATL51	29.747%	Swiss-Prot	weak database homology
`Q9ZV53`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL49	33.333%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card