LXL04_013692 | RubberDandelionOmics

Gene overview

LXL04_013692

Reference: OH-1004 Chr: Chr03 Coordinates: 34243861-34246303 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1347 bp · LXL04_013692|LXL04_013692|OH1004|cDNA

ATGTTTTTTATGATTATGGTTCATAACTCATATGCGTTACAATGTCGTCATACGTTATGTTTCTGCTCGATTTTATTCTGTGAGCCGTCAACACCCTGCAACTATCGTCATACTTACAACAACATGTACGAGCATTTCTGCAGGGAtcatttcttttattttgtACCATTCTTATACAACAAAGATGAGAAATTAATGAAGGCGGATAGACATGCGTTTATCACTAGTTTATTCTTCAGAATACGTAAAAGTCTTGCATC...

CDS

Download CDS FASTA

1347 bp · LXL04_013692|LXL04_013692|OH1004|CDS

ATGTTTTTTATGATTATGGTTCATAACTCATATGCGTTACAATGTCGTCATACGTTATGTTTCTGCTCGATTTTATTCTGTGAGCCGTCAACACCCTGCAACTATCGTCATACTTACAACAACATGTACGAGCATTTCTGCAGGGATCATTTCTTTTATTTTGTACCATTCTTATACAACAAAGATGAGAAATTAATGAAGGCGGATAGACATGCGTTTATCACTAGTTTATTCTTCAGAATACGTAAAAGTCTTGCATC...

Protein

Download Protein FASTA

448 aa · LXL04_013692|LXL04_013692|OH1004|PROTEIN

MFFMIMVHNSYALQCRHTLCFCSILFCEPSTPCNYRHTYNNMYEHFCRDHFFYFVPFLYNKDEKLMKADRHAFITSLFFRIRKSLASRSADVANKRPRVNEPSSSHSRMVHHARRLSQIYRSSQITDGTHMTPVQVDSDSDPDSDSDAESDLDPEADQDDGADGVAEAQHQHLDHHTTTSAATSLPGQATSTPAVAREEIQAVVTDPDMLHCSICHNSLCPPIYLCDNGHTSCTSCKTRSKNTCPSCSIPKGFNRCRGMD...

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_013692`
TK1151 ID	TkA02G478120
OH-1004 ID	LXL04_013692
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 83.699 / OH-1004 59.598 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_013692

Location Chr03:34243861-34246303 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At5g37870`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At1g66630`	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
`At5g37890`	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

View annotation sources

Functional annotation source: OH1004 · LXL04_013692 · 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:AT1G66630

ath:AT5G37870

ath:AT5G37890

ath:AT5G37930

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.

Nucleus0.537

Rank 1 · LXL04_013692 · OH-1004

Cytoplasm0.516

Rank 2 · LXL04_013692 · OH-1004

Mitochondrion0.052

Rank 3 · LXL04_013692 · OH-1004

Cell membrane0.046

Rank 4 · LXL04_013692 · OH-1004

Endoplasmic reticulum0.034

Rank 5 · LXL04_013692 · 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.

PF21362.4Sina_RING212-247 aa

PF21361.4Sina_ZnF261-328 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013692	`PF21362.4`	Sina_RING	212	247	1.7e-07	32.0
LXL04_013692	`PF21361.4`	Sina_ZnF	261	328	4e-08	34.2

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	32.016%	Swiss-Prot	moderate database homology
`Q9FKD9`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINA-like 6	34.184%	Swiss-Prot	weak database homology
`Q9C6H2`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 3	33.333%	Swiss-Prot	moderate database homology
`Q9C6H3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 2	29.963%	Swiss-Prot	weak database homology
`Q9FKD7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 7	26.766%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card