LXL04_008753 | RubberDandelionOmics

Gene overview

LXL04_008753

Reference: OH-1004 Chr: Chr02 Coordinates: 108086429-108087817 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1389 bp · LXL04_008753|LXL04_008753|OH1004|cDNA

ATGCAAAATCCCCTGTCCAGCAAATATCTTATTACCACCAAATCCATCCTATTTTACTCCTCTTCCTTTCCTTGCCTGAAACACCCACCCGTAAAGCACACCCCTCTGGCCCCAATGGCGGATGTCTCCTACCACCATGACGACGACGACAATGACGATCGGCAAGATGTTCTAGTATCCTATTCTCACTGGCCCGACGATCTTGAAGGATTCGACGTTTACCCTCCAGATCTTGACATCCCTTCCTCCCAAGATGTCTT...

CDS

Download CDS FASTA

1389 bp · LXL04_008753|LXL04_008753|OH1004|CDS

ATGCAAAATCCCCTGTCCAGCAAATATCTTATTACCACCAAATCCATCCTATTTTACTCCTCTTCCTTTCCTTGCCTGAAACACCCACCCGTAAAGCACACCCCTCTGGCCCCAATGGCGGATGTCTCCTACCACCATGACGACGACGACAATGACGATCGGCAAGATGTTCTAGTATCCTATTCTCACTGGCCCGACGATCTTGAAGGATTCGACGTTTACCCTCCAGATCTTGACATCCCTTCCTCCCAAGATGTCTT...

Protein

Download Protein FASTA

462 aa · LXL04_008753|LXL04_008753|OH1004|PROTEIN

MQNPLSSKYLITTKSILFYSSSFPCLKHPPVKHTPLAPMADVSYHHDDDDNDDRQDVLVSYSHWPDDLEGFDVYPPDLDIPSSQDVFCGPRRRLDRNPPRISPLDRETQANFVIDMFHQRVEQSQSQSQPQSHSTPRVIEENRSDRSLGVVEGNEDVNSNEFQVDFVSELGFHVENHDNHNVNGVDGDYSGFTIAETGDEFLVSRRRMDRHAARSESSRSSIDSGAPGFFMGGLTVTDMAEDGPAMDRDCDDETSLHLCW...

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_008753`
TK1151 ID	TkA03G337510
OH-1004 ID	LXL04_008753
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 95.692 / OH-1004 67.316 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_008753

Location Chr02:108086429-108087817 (+)

Description Similar to RING1: E3 ubiquitin-protein ligase RING1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19950`	E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.	No verified direct reference in this release
`At5g64920`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein.1999 · DOI: 10.1074/jbc.274.39.27674 Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8).2002 · DOI: 10.1046/j.1365-313x.2002.01298.x
`At2g40830`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0488800`	Possesses E3 ubiqutin-protein ligase activity in vitro.	Molecular dissection of Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress.2016 · DOI: 10.1111/ppl.12459

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008753 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009938 negative regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0090378 seed trichome elongation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G40830

ath:AT3G19950

ath:AT5G64920

dosa:Os05g0488800

osa:4339152

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.

Cytoplasm0.559

Rank 1 · LXL04_008753 · OH-1004

Nucleus0.477

Rank 2 · LXL04_008753 · OH-1004

Cell membrane0.074

Rank 3 · LXL04_008753 · OH-1004

Endoplasmic reticulum0.072

Rank 4 · LXL04_008753 · OH-1004

Lysosome / Vacuole0.049

Rank 5 · LXL04_008753 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13639.13zf-RING_2403-445 aa

PF12678.14zf-rbx1403-445 aa

PF13923.13zf-C3HC4_2404-444 aa

PF17123.12zf-RING_11404-431 aa

PF00097.32zf-C3HC4404-444 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008753	`PF13639.13`	zf-RING_2	403	445	1e-12	48.8
LXL04_008753	`PF12678.14`	zf-rbx1	403	445	6.2e-08	33.5
LXL04_008753	`PF13923.13`	zf-C3HC4_2	404	444	7.2e-09	36.0
LXL04_008753	`PF17123.12`	zf-RING_11	404	431	3.5e-08	33.7
LXL04_008753	`PF00097.32`	zf-C3HC4	404	444	6.8e-08	33.0

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
`Q8LPN7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1-like	41.985%	Swiss-Prot	weak database homology
`Q9SPL2`	Arabidopsis thaliana	E3 ubiquitin-protein ligase CIP8	57.831%	Swiss-Prot	weak database homology
`O22197`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHC1A	43.689%	Swiss-Prot	weak database homology
`Q6AVN2`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase SIRP1	43.617%	Swiss-Prot	weak database homology

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