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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_021921
Reference: OH-1004 Chr: Chr04 Coordinates: 140293552-140294679 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1128 bp · LXL04_021921|LXL04_021921|OH1004|cDNA

ATGTCAATGGATAGCTCTTCTTCGTCGTCATACTGGTGTTACAGATGCCGACGATTCATCGATGTTCCTACTCACCTGCTAGATTCTTCTTTCTTTTGCCCGGATTGTAATGGTGGATTCGTAGAGGACATCGGTAGCCCGACCCAGATACCCGAATCACCACTTTCGGATTCTCACCGGAGACGTTTTCCGGCGGCGGCACTGTACAGGGACGAAAACGAGCAACAGAGCCCACCGGTGCTCCGCCGTGCTAGAAGGAA...

CDS

Download CDS FASTA

1128 bp · LXL04_021921|LXL04_021921|OH1004|CDS

ATGTCAATGGATAGCTCTTCTTCGTCGTCATACTGGTGTTACAGATGCCGACGATTCATCGATGTTCCTACTCACCTGCTAGATTCTTCTTTCTTTTGCCCGGATTGTAATGGTGGATTCGTAGAGGACATCGGTAGCCCGACCCAGATACCCGAATCACCACTTTCGGATTCTCACCGGAGACGTTTTCCGGCGGCGGCACTGTACAGGGACGAAAACGAGCAACAGAGCCCACCGGTGCTCCGCCGTGCTAGAAGGAA...

Protein

Download Protein FASTA

375 aa · LXL04_021921|LXL04_021921|OH1004|PROTEIN

MSMDSSSSSSYWCYRCRRFIDVPTHLLDSSFFCPDCNGGFVEDIGSPTQIPESPLSDSHRRRFPAAALYRDENEQQSPPVLRRARRNAGDRSPFNPVIVLRGNTPTVDSRNQGGEGGGFEMYYDDGAGSGLRPVPVSMSEFLLGAGFDRLLDQLTQIESNGLGRIDQNPPASKAAIEALPTIEIQEIHTFTESHCAVCKDAFELQTEAKEMPCKHLYHSDCILPWLTLRNSCPVCRHELPPENQDSVSDDEALGLTIWRL...

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_021921
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_021921
LocationChr04:140293552-140294679 (+)
DescriptionSimilar to RHC2A: Probable E3 ubiquitin-protein ligase RHC2A
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g39720 Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. No verified direct reference in this release
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
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

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_021921 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006970 response to osmotic stress Biological Process
GO:0009414 response to water deprivation Biological Process
GO:0009737 response to abscisic acid Biological Process
GO:0009738 abscisic acid-activated 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:0090378 seed trichome elongation Biological Process
GO:1902006 negative regulation of L-proline biosynthetic process Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0005829 cytosol Cellular Component
KEGG gene cross-reference
ath:AT2G39720
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.

Cytoplasm0.464
Rank 1 · LXL04_021921 · OH-1004
Nucleus0.366
Rank 2 · LXL04_021921 · OH-1004
Cell membrane0.168
Rank 3 · LXL04_021921 · OH-1004
Lysosome / Vacuole0.113
Rank 4 · LXL04_021921 · OH-1004
Endoplasmic reticulum0.103
Rank 5 · LXL04_021921 · 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_199-44 aa
PF12678.14zf-rbx1193-236 aa
PF13639.13zf-RING_2194-236 aa
PF13923.13zf-C3HC4_2195-235 aa
PF00097.32zf-C3HC4195-235 aa
PF06547.18DUF1117254-358 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_021921PF14369.12Zn_ribbon_199441.9e-1247.8
LXL04_021921PF12678.14zf-rbx11932366.2e-0730.3
LXL04_021921PF13639.13zf-RING_21942363.4e-1143.9
LXL04_021921PF13923.13zf-C3HC4_21952352.3e-0834.4
LXL04_021921PF00097.32zf-C3HC41952359.7e-0729.3
LXL04_021921PF06547.18DUF11172543589.9e-2691.2

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
O22283Arabidopsis thalianaProbable E3 ubiquitin-protein ligase RHC2A48.903%Swiss-Protmoderate database homology
Q9SNB6Arabidopsis thalianaE3 ubiquitin-protein ligase RDUF149.515%Swiss-Protmoderate database homology
Q940T5Arabidopsis thalianaE3 ubiquitin-protein ligase RDUF249.032%Swiss-Protmoderate database homology
Q94AK4Arabidopsis thalianaE3 ubiquitin-protein ligase RZF135.802%Swiss-Protmoderate database homology

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