RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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_000574
Reference: OH-1004 Chr: Chr01 Coordinates: 10442210-10446387 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1230 bp · LXL04_000574|LXL04_000574|OH1004|cDNA

ATGTCAAGGACAACGGCGGCGTCTTATTGGTGCTACAGATGCTCGCGGTTCGTCAGAGTATCGGCGGAAGACACCGTTTTGTGTCCATACTGTGAGGGTGGATTCTTGGAGGCTGTTGAAGCCAGCGAGCCTCCACCACTGGGGACACGCCGGAGGTTTCCTGCCTCGGCGATGTACATGCTTGGAAACAACGACCGATCAGATCTACGGTCACGGCGTGGTGGTCGGCGTAACAACGGAGACAGGTCTCCGTTCAATCC...

CDS

Download CDS FASTA

1230 bp · LXL04_000574|LXL04_000574|OH1004|CDS

ATGTCAAGGACAACGGCGGCGTCTTATTGGTGCTACAGATGCTCGCGGTTCGTCAGAGTATCGGCGGAAGACACCGTTTTGTGTCCATACTGTGAGGGTGGATTCTTGGAGGCTGTTGAAGCCAGCGAGCCTCCACCACTGGGGACACGCCGGAGGTTTCCTGCCTCGGCGATGTACATGCTTGGAAACAACGACCGATCAGATCTACGGTCACGGCGTGGTGGTCGGCGTAACAACGGAGACAGGTCTCCGTTCAATCC...

Protein

Download Protein FASTA

409 aa · LXL04_000574|LXL04_000574|OH1004|PROTEIN

MSRTTAASYWCYRCSRFVRVSAEDTVLCPYCEGGFLEAVEASEPPPLGTRRRFPASAMYMLGNNDRSDLRSRRGGRRNNGDRSPFNPVIVLRGPAEGNGAVEESGGGERGFELYYDDGAGSGLQPLPPTMSEFLMGSGFARLLDQLSQIEMNGLGRPGHPPASKAAIESMPMVEISEVHVSTESHCAVCKEAFVLRAEAREMPCKHIYHSDCILPWLALRNSCPVCRHELPTDSTDSNSSNPERSESNEEESAAVGLTIW...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_000574
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_000574
LocationChr01:10442210-10446387 (+)
DescriptionSimilar to RDUF1: E3 ubiquitin-protein ligase RDUF1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g46620 E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid-dependent drought stress responses.
Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces tolerance to ABA-mediated drought stress.2012 · DOI: 10.1016/j.bbrc.2012.02.131
The E3 ligase AtRDUF1 positively regulates salt stress responses in Arabidopsis thaliana.2013 · DOI: 10.1371/journal.pone.0071078
At2g39720 Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. No verified direct reference in this release
At5g59550 E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid-dependent drought stress responses.
Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces tolerance to ABA-mediated drought stress.2012 · DOI: 10.1016/j.bbrc.2012.02.131
At3g56580 E3 ubiquitin-protein ligase that promotes osmotic stress and abscisic acid (ABA) responses.
The atrzf1 mutation of the novel RING-type E3 ubiquitin ligase increases proline contents and enhances drought tolerance in Arabidopsis.2013 · DOI: 10.1016/j.plantsci.2012.12.007
PCA22 acts as a suppressor of atrzf1 to mediate proline accumulation in response to abiotic stress in Arabidopsis.2017 · DOI: 10.1093/jxb/erx069
At2g40830 Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. 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_000574 · 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:0009414 response to water deprivation Biological Process
GO:0009651 response to salt stress Biological Process
GO:0009737 response to abscisic acid Biological Process
GO:0009738 abscisic acid-activated signaling pathway Biological Process
GO:0009938 negative regulation of gibberellic acid mediated signaling pathway Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0047484 regulation of response to osmotic stress Biological Process
GO:0051865 protein autoubiquitination Biological Process
GO:1902006 negative regulation of L-proline biosynthetic process Biological Process
GO:0005634 nucleus Cellular Component
KEGG gene cross-reference
ath:AT2G39720
ath:AT2G40830
ath:AT3G46620
ath:AT3G56580
ath:AT5G59550
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.

Cytoplasm0.543
Rank 1 · LXL04_000574 · OH-1004
Nucleus0.379
Rank 2 · LXL04_000574 · OH-1004
Cell membrane0.159
Rank 3 · LXL04_000574 · OH-1004
Endoplasmic reticulum0.083
Rank 4 · LXL04_000574 · OH-1004
Lysosome / Vacuole0.071
Rank 5 · LXL04_000574 · 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.

PF14369.12Zn_ribbon_198-37 aa
PF12678.14zf-rbx1184-227 aa
PF13639.13zf-RING_2185-227 aa
PF13923.13zf-C3HC4_2186-226 aa
PF00097.32zf-C3HC4186-226 aa
PF06547.18DUF1117255-364 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_000574PF14369.12Zn_ribbon_198378.7e-1348.9
LXL04_000574PF12678.14zf-rbx11842274.2e-0627.6
LXL04_000574PF13639.13zf-RING_21852273.6e-1143.9
LXL04_000574PF13923.13zf-C3HC4_21862262.5e-0731.1
LXL04_000574PF00097.32zf-C3HC41862268.9e-0626.2
LXL04_000574PF06547.18DUF11172553643.7e-38131.2

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9SNB6Arabidopsis thalianaE3 ubiquitin-protein ligase RDUF149.728%Swiss-Protmoderate database homology
O22283Arabidopsis thalianaProbable E3 ubiquitin-protein ligase RHC2A51.662%Swiss-Protstrong database homology
Q940T5Arabidopsis thalianaE3 ubiquitin-protein ligase RDUF249.444%Swiss-Protmoderate database homology
Q94AK4Arabidopsis thalianaE3 ubiquitin-protein ligase RZF136.170%Swiss-Protmoderate database homology
O22197Arabidopsis thalianaProbable E3 ubiquitin-protein ligase RHC1A34.661%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser