LXL04_008946 | RubberDandelionOmics

Gene overview

LXL04_008946

Reference: OH-1004 Chr: Chr02 Coordinates: 113592336-113592746 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

411 bp · LXL04_008946|LXL04_008946|OH1004|cDNA

ATGCCTACAAACCTAGTAGTCTCGTTTCTTACTCATTTGAAATGGGCACTTGAATTCTTGACTCATCATATTTTTTTCCACCACCGTATGGTTGGTGTACAGCCGGAGAACCACCACCATGGTGGTGGCGGAGGTGCAGCCCTTTTTGATGAGGTAGAGTGTGGTGTCTGCTCAAGGAAAatcgaagatgatgatgagaTGAGAGAGTCGAGGTGCAACCACTTTTTTCACAAACATTGCTTGGATGTGTGGGTTACATG...

CDS

Download CDS FASTA

411 bp · LXL04_008946|LXL04_008946|OH1004|CDS

ATGCCTACAAACCTAGTAGTCTCGTTTCTTACTCATTTGAAATGGGCACTTGAATTCTTGACTCATCATATTTTTTTCCACCACCGTATGGTTGGTGTACAGCCGGAGAACCACCACCATGGTGGTGGCGGAGGTGCAGCCCTTTTTGATGAGGTAGAGTGTGGTGTCTGCTCAAGGAAAATCGAAGATGATGATGAGATGAGAGAGTCGAGGTGCAACCACTTTTTTCACAAACATTGCTTGGATGTGTGGGTTACATG...

Protein

Download Protein FASTA

136 aa · LXL04_008946|LXL04_008946|OH1004|PROTEIN

MPTNLVVSFLTHLKWALEFLTHHIFFHHRMVGVQPENHHHGGGGGAALFDEVECGVCSRKIEDDDEMRESRCNHFFHKHCLDVWVTCRRTTCPLCHDNLAKIDGGHGRTIIGGWEVLYFDYCNACPDGDYGSWWLR

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_008946`
TK1151 ID	TkA03G306170
OH-1004 ID	LXL04_008946
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	68.400
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_008946

Location Chr02:113592336-113592746 (+)

Description Similar to SPBP4H10.07: Uncharacterized RING finger protein P4H10.07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g05200`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At1g72220`	RING-H2 finger protein ATL54.	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
`At2g04240`	Function on abscisic acid homeostasis at post-translational level, probably through ubiquitin/proteasome-dependent substrate- specific degradation.	Upregulation of an Arabidopsis RING-H2 gene, XERICO, confers drought tolerance through increased abscisic acid biosynthesis.2006 · DOI: 10.1111/j.1365-313x.2006.02782.x Global analysis of della direct targets in early gibberellin signaling in Arabidopsis.2007 · DOI: 10.1105/tpc.107.054999

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008946 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009687 abscisic acid metabolic process Biological Process

GO:0009688 abscisic acid biosynthetic process Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0033591 response to L-ascorbic acid Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005576 extracellular region Cellular Component

KEGG gene cross-reference

ath:AT1G22500

ath:AT1G72220

ath:AT2G04240

ath:AT3G05200

spo:2541304

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.

Cytoplasm0.387

Rank 1 · LXL04_008946 · OH-1004

Nucleus0.368

Rank 2 · LXL04_008946 · OH-1004

Cell membrane0.219

Rank 3 · LXL04_008946 · OH-1004

Endoplasmic reticulum0.117

Rank 4 · LXL04_008946 · OH-1004

Lysosome / Vacuole0.094

Rank 5 · LXL04_008946 · 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.

PF13639.13zf-RING_253-95 aa

PF17123.12zf-RING_1153-81 aa

PF12678.14zf-rbx154-95 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008946	`PF13639.13`	zf-RING_2	53	95	2.1e-09	38.2
LXL04_008946	`PF17123.12`	zf-RING_11	53	81	5e-07	30.0
LXL04_008946	`PF12678.14`	zf-rbx1	54	95	3e-07	31.3

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
`Q8RXX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL6	44.231%	Swiss-Prot	weak database homology
`Q8LFY8`	Arabidopsis thaliana	RING-H2 finger protein ATL54	38.983%	Swiss-Prot	weak database homology
`Q9SK92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL15	40.000%	Swiss-Prot	weak database homology
`Q9SI09`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase XERICO	40.741%	Swiss-Prot	weak database homology

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