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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_017790
Reference: OH-1004 Chr: Chr04 Coordinates: 1257027-1259933 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1944 bp · LXL04_017790|LXL04_017790|OH1004|cDNA

ATGGCGGAAGAAGGAGAAAAAGGTGGATTGATGCAAAATTTGATTGATATCGTAAACGAGATATCTGCAATCTCCGACTACCGGTATACCGTGAAGAAGCTTTTCTCTAATCTAGCTAGGAGGGTAAAGCTTTTAATTCCACTGTTTGAAGAAATCCGTGATATTAATGAGCCACTCCCTGATTGCTCTCATGAAGCCTTGGTTTCGTTAATGGAGGCTATGGAATCTGCTAAGGAATTGCTTCGCATCGGGAGTGAAGG...

CDS

Download CDS FASTA

1944 bp · LXL04_017790|LXL04_017790|OH1004|CDS

ATGGCGGAAGAAGGAGAAAAAGGTGGATTGATGCAAAATTTGATTGATATCGTAAACGAGATATCTGCAATCTCCGACTACCGGTATACCGTGAAGAAGCTTTTCTCTAATCTAGCTAGGAGGGTAAAGCTTTTAATTCCACTGTTTGAAGAAATCCGTGATATTAATGAGCCACTCCCTGATTGCTCTCATGAAGCCTTGGTTTCGTTAATGGAGGCTATGGAATCTGCTAAGGAATTGCTTCGCATCGGGAGTGAAGG...

Protein

Download Protein FASTA

647 aa · LXL04_017790|LXL04_017790|OH1004|PROTEIN

MAEEGEKGGLMQNLIDIVNEISAISDYRYTVKKLFSNLARRVKLLIPLFEEIRDINEPLPDCSHEALVSLMEAMESAKELLRIGSEGSKIYLVLERDQIMTRYHEITAGLEQHITGISFNNLDISDEVKEQVELVLAQFKRAKGRIDTPDIQLYEDLSSLYNKDINEEEEDPAVLNRLAENLHLTEITDLTNESIALHEMVTLTGDPEETIEKMSLLLKRIKDFIQTETPVLEASTDLPSCTLVKNHKNSIIPDDFRCPI...

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.

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ID Mapping

Input IDLXL04_017790
Source versionOH-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 IDLXL04_017790
LocationChr04:1257027-1259933 (-)
DescriptionSimilar to PUB13: U-box domain-containing protein 13
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g46510 Functions as an E3 ubiquitin ligase. No verified direct reference in this release
At2g28830 Functions as an E3 ubiquitin ligase. No verified direct reference in this release
At3g54850 Functions as an E3 ubiquitin ligase with specific E2 ubiquitin-conjugating enzymes.
Structure and biochemical function of a prototypical Arabidopsis U-box domain.2004 · DOI: 10.1074/jbc.m405057200

Rice

Reference gene IDPossible functionPapers / DOI
Os12g0570000 E3 ubiquitin-protein ligase that negatively regulates programmed cell death and disease resistance.
Spotted leaf11, a negative regulator of plant cell death and defense, encodes a U-box/armadillo repeat protein endowed with E3 ubiquitin ligase activity.2004 · DOI: 10.1105/tpc.104.025171
SPIN1, a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11, is involved in flowering time control in rice.2008 · DOI: 10.1105/tpc.108.058610
UniProt: A2ZLU6 Defense related protein that negatively regulates programmed cell death. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_017790 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006952 defense response Biological Process
GO:0007166 cell surface receptor signaling pathway Biological Process
GO:0009908 flower development Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0031348 negative regulation of defense response Biological Process
GO:0042742 defense response to bacterium Biological Process
GO:0043069 negative regulation of programmed cell death Biological Process
GO:0048586 regulation of long-day photoperiodism, flowering Biological Process
GO:0050777 negative regulation of immune response Biological Process
GO:2000028 regulation of photoperiodism, flowering Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
KEGG gene cross-reference
ath:AT2G28830
ath:AT3G46510
ath:AT3G54850
dosa:Os12g0570000
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.

Cytoplasm0.603
Rank 1 · LXL04_017790 · OH-1004
Nucleus0.311
Rank 2 · LXL04_017790 · OH-1004
Cell membrane0.222
Rank 3 · LXL04_017790 · OH-1004
Golgi apparatus0.063
Rank 4 · LXL04_017790 · OH-1004
Endoplasmic reticulum0.058
Rank 5 · LXL04_017790 · 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.

PF25368.2PUB10_N32-143 aa
PF04564.22U-box252-322 aa
PF25598.2ARM_PUB346-620 aa
PF24768.2ARM_ARMC5359-521 aa
PF00514.30Arm375-414 aa
PF24768.2ARM_ARMC5376-578 aa
PF00514.30Arm417-455 aa
PF00514.30Arm459-496 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_017790PF25368.2PUB10_N321432.1e-34119.5
LXL04_017790PF04564.22U-box2523221.9e-2383.1
LXL04_017790PF25598.2ARM_PUB3466203.3e-29103.0
LXL04_017790PF24768.2ARM_ARMC53595218.6e-2485.1
LXL04_017790PF00514.30Arm3754141.5e-39133.5
LXL04_017790PF24768.2ARM_ARMC53765788.6e-2485.1
LXL04_017790PF00514.30Arm4174551.5e-39133.5
LXL04_017790PF00514.30Arm4594961.5e-39133.5
LXL04_017790PF00514.30Arm5405791.5e-39133.5

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9SNC6Arabidopsis thalianaU-box domain-containing protein 1365.496%Swiss-Protstrong database homology
Q9ZV31Arabidopsis thalianaU-box domain-containing protein 1260.156%Swiss-Protstrong database homology
Q8VZ40Arabidopsis thalianaU-box domain-containing protein 1452.922%Swiss-Protstrong database homology
Q0IMG9Oryza sativa subsp. japonicaE3 ubiquitin-protein ligase SPL1164.899%Swiss-Protstrong database homology
A2ZLU6Oryza sativa subsp. indicaProtein spotted leaf 1164.899%Swiss-Protstrong database homology

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