LXL04_030709 | RubberDandelionOmics

Gene overview

LXL04_030709

Reference: OH-1004 Chr: Chr06 Coordinates: 121136336-121138700 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1104 bp · LXL04_030709|LXL04_030709|OH1004|cDNA

ATGGCGGTCAGGGGCGTCGATTTTAAGTGGTACGATGGGTTTTTCCTGTCTATGCTTGCCACTAGTATAATTATAGTTGCAATCAACTGGAAACGTTACCATCTATGCACACATCCACTACATATCTGGATCGTGGTTGATTATACCACAGTCTTCATATTTCGTCTGTTGATGTTTGTCGACAATGGGCTTGCAGCTGGAATGGGATTAGATTTCGGCCGGCAGCAGAGACAAGCTCGGTTCTGTGGAAGAGCGGTGGT...

CDS

Download CDS FASTA

1104 bp · LXL04_030709|LXL04_030709|OH1004|CDS

ATGGCGGTCAGGGGCGTCGATTTTAAGTGGTACGATGGGTTTTTCCTGTCTATGCTTGCCACTAGTATAATTATAGTTGCAATCAACTGGAAACGTTACCATCTATGCACACATCCACTACATATCTGGATCGTGGTTGATTATACCACAGTCTTCATATTTCGTCTGTTGATGTTTGTCGACAATGGGCTTGCAGCTGGAATGGGATTAGATTTCGGCCGGCAGCAGAGACAAGCTCGGTTCTGTGGAAGAGCGGTGGT...

Protein

Download Protein FASTA

367 aa · LXL04_030709|LXL04_030709|OH1004|PROTEIN

MAVRGVDFKWYDGFFLSMLATSIIIVAINWKRYHLCTHPLHIWIVVDYTTVFIFRLLMFVDNGLAAGMGLDFGRQQRQARFCGRAVVLSILSIFLYPFLWAWTVIGSLWFTSSKNCLPEEGQKWGFLIWLLFSYSGLVCIAALCTKKWLNRRKAHSLRAQQGIPVSEYGVLVDMVRVPDWAFETAIGQEMRGMAQDAATSYHPGLYLTEPQREAVEALIQELPKFMLKAVPTDCSECPICLEEFHVGNEVRGLPCAHNFH...

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_030709`
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_030709

Location Chr06:121136336-121138700 (+)

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
`At2g17730`	Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.	No verified direct reference in this release
`At5g66070`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At3g18930`	RING-H2 finger protein ATL65.	No verified direct reference in this release
`At2g35910`	RING-H2 finger protein ATL70.	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_030709 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0031982 vesicle Cellular Component

KEGG gene cross-reference

ath:AT2G17730

ath:AT2G35910

ath:AT3G18930

ath:AT3G47990

ath:AT5G66070

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.

Cytoplasm0.275

Rank 1 · LXL04_030709 · OH-1004

Endoplasmic reticulum0.267

Rank 2 · LXL04_030709 · OH-1004

Golgi apparatus0.264

Rank 3 · LXL04_030709 · OH-1004

Cell membrane0.234

Rank 4 · LXL04_030709 · OH-1004

Lysosome / Vacuole0.219

Rank 5 · LXL04_030709 · 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_2236-278 aa

PF17123.12zf-RING_11236-264 aa

PF13923.13zf-C3HC4_2236-277 aa

PF13445.13zf-RING_UBOX237-275 aa

PF00097.32zf-C3HC4237-277 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030709	`PF26753.1`	SIS3_N	11	161	2e-68	229.7
LXL04_030709	`PF13639.13`	zf-RING_2	236	278	7.5e-14	52.4
LXL04_030709	`PF17123.12`	zf-RING_11	236	264	3.9e-10	40.0
LXL04_030709	`PF13923.13`	zf-C3HC4_2	236	277	1.2e-08	35.3
LXL04_030709	`PF13445.13`	zf-RING_UBOX	237	275	7.2e-08	33.0
LXL04_030709	`PF00097.32`	zf-C3HC4	237	277	1.4e-07	31.9

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
`Q8GYT9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SIS3	71.944%	Swiss-Prot	strong database homology
`Q8GT74`	Arabidopsis thaliana	NEP1-interacting protein 2	38.462%	Swiss-Prot	weak database homology
`Q9FKX5`	Arabidopsis thaliana	NEP1-interacting protein-like 1	35.897%	Swiss-Prot	weak database homology
`Q67YI6`	Arabidopsis thaliana	RING-H2 finger protein ATL65	30.263%	Swiss-Prot	weak database homology
`Q8RX29`	Arabidopsis thaliana	RING-H2 finger protein ATL70	41.304%	Swiss-Prot	weak database homology

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