LXL04_007013 | RubberDandelionOmics

Gene overview

LXL04_007013

Reference: OH-1004 Chr: Chr02 Coordinates: 33703625-33713564 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2273 bp · LXL04_007013|LXL04_007013|OH1004|cDNA

ATGATGCGGTTGCGTGTGAAAAATCAGATAAACGATGGATCCCCAGCATCGACGGCCTCCACGAATCAAAACACTTCTAGGGGAGTTGAAAGTGCGATAACGATGGTGAGATTTTCAATCGGCGAAGACGACGAAGATGCTCCACTTGCCAATAAACGGCCACGATTCGGCGAACCTGCATCTCAATCACAACCGCCAGTTGTGGCGGGGgaagaggaggaagaggagATGATTCCAATAGAAGATGTAGAATCGGATAC...

CDS

Download CDS FASTA

2262 bp · LXL04_007013|LXL04_007013|OH1004|CDS

ATGATGCGGTTGCGTGTGAAAAATCAGATAAACGATGGATCCCCAGCATCGACGGCCTCCACGAATCAAAACACTTCTAGGGGAGTTGAAAGTGCGATAACGATGGTGAGATTTTCAATCGGCGAAGACGACGAAGATGCTCCACTTGCCAATAAACGGCCACGATTCGGCGAACCTGCATCTCAATCACAACCGCCAGTTGTGGCGGGGGAAGAGGAGGAAGAGGAGATGATTCCAATAGAAGATGTAGAATCGGATAC...

Protein

Download Protein FASTA

753 aa · LXL04_007013|LXL04_007013|OH1004|PROTEIN

MMRLRVKNQINDGSPASTASTNQNTSRGVESAITMVRFSIGEDDEDAPLANKRPRFGEPASQSQPPVVAGEEEEEEMIPIEDVESDTEGSEEEEDDEDDESEAVEEDDEEEEDAGSEEDVVQFTDVQPERQNRPVVLSNIPSSNITDQIRSCFTAPPVFNNATGALHVVLTDPDVLDCPICLDPLSTPVFQCENGHIACSSCCTKVKRKCPSCCMPIGYNRCRAIEKVLESIKISCKNSRSGCKETIPYSKKIDHEETCP...

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_007013`
TK1151 ID	TkA03G103320
OH-1004 ID	LXL04_007013
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	57.100
Protein coverage (%)	TK1151 97.768 / OH-1004 28.818 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_007013

Location Chr02:33703625-33713564 (-)

Description Similar to At5g37930: E3 ubiquitin-protein ligase SINA-like 10

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g37930`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g37890`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g37870`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g37910`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At1g66620`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_007013 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009411 response to UV Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G66620

ath:AT5G37870

ath:AT5G37890

ath:AT5G37910

ath:AT5G37930

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.

Nucleus0.668

Rank 1 · LXL04_007013 · OH-1004

Cytoplasm0.340

Rank 2 · LXL04_007013 · OH-1004

Cell membrane0.066

Rank 3 · LXL04_007013 · OH-1004

Endoplasmic reticulum0.040

Rank 4 · LXL04_007013 · OH-1004

Mitochondrion0.036

Rank 5 · LXL04_007013 · 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.

PF21362.4Sina_RING178-213 aa

PF21361.4Sina_ZnF227-294 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007013	`PF21362.4`	Sina_RING	178	213	4.5e-11	43.4
LXL04_007013	`PF21361.4`	Sina_ZnF	227	294	8.1e-12	46.1

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
`Q84K34`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 10	33.245%	Swiss-Prot	weak database homology
`Q9FKD7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 7	34.836%	Swiss-Prot	weak database homology
`Q9FKD9`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINA-like 6	33.871%	Swiss-Prot	weak database homology
`Q9FKD5`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINA-like 9	35.965%	Swiss-Prot	weak database homology
`Q9C6H3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 2	33.333%	Swiss-Prot	weak database homology

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