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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_011822
Reference: OH-1004 Chr: Chr03 Coordinates: 879699-882176 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

987 bp · LXL04_011822|LXL04_011822|OH1004|cDNA

ATGGATTTGGATAATATAGAGTGTGTATCTTCTTCCAGTGGAGTAGAAGGTGCAGAGATCCAATCGCAACTTACTCAAAATTCCGCTCCCAAGCCTCGTAATAACACGGGAATGCCTCCTGGTACTAGTGTTCATGAACTGTTAGAGTGCCCCGTTTGTACCGGTTCAATGTACCCTCCAATCCATCAGTGTCACAATGGACACACATTATGCTCGACCTGTAAAACACAAGTGCACAACCGGTGCCCGACTTGCAGACA...

CDS

Download CDS FASTA

987 bp · LXL04_011822|LXL04_011822|OH1004|CDS

ATGGATTTGGATAATATAGAGTGTGTATCTTCTTCCAGTGGAGTAGAAGGTGCAGAGATCCAATCGCAACTTACTCAAAATTCCGCTCCCAAGCCTCGTAATAACACGGGAATGCCTCCTGGTACTAGTGTTCATGAACTGTTAGAGTGCCCCGTTTGTACCGGTTCAATGTACCCTCCAATCCATCAGTGTCACAATGGACACACATTATGCTCGACCTGTAAAACACAAGTGCACAACCGGTGCCCGACTTGCAGACA...

Protein

Download Protein FASTA

328 aa · LXL04_011822|LXL04_011822|OH1004|PROTEIN

MDLDNIECVSSSSGVEGAEIQSQLTQNSAPKPRNNTGMPPGTSVHELLECPVCTGSMYPPIHQCHNGHTLCSTCKTQVHNRCPTCRQELGDIRCLALEKVAESLELPCRYYSLGCPETFPYYSKLKHEMLCNCRPYNCPYAGSECSVTGDIPFLVTHLRDDHKVDMHSGCTFNHRYVKSNPREVENATWMLTVFNCFGEYFCLHFEAFQLGVAPVYMAFVRFMGDEVAARSYSYSLEVGGNGRKLIWEGTPRSIRDSHRK...

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_011822
TK1151 IDTkA02G610340
OH-1004 IDLXL04_011822
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)100.000
Protein coverage (%)TK1151 97.436 / OH-1004 92.683
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 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_011822
LocationChr03:879699-882176 (+)
DescriptionSimilar to SINAT3: E3 ubiquitin-protein ligase SINAT3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g61790 E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.
SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267
At4g27880 E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.
SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267
At5g53360 E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.
SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals.2002 · DOI: 10.1038/nature00998
SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants.2020 · DOI: 10.1111/jipb.13005
At3g58040 E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.
TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis.2017 · DOI: 10.1105/tpc.17.00056
SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267

Rice

Reference gene IDPossible functionPapers / DOI
Os03g0356414 E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.
The SINA E3 ligase OsDIS1 negatively regulates drought response in rice.2011 · DOI: 10.1104/pp.111.180893
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_011822 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006511 ubiquitin-dependent protein catabolic process Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0080148 negative regulation of response to water deprivation Biological Process
GO:2000785 regulation of autophagosome assembly Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0005771 multivesicular body Cellular Component
GO:0005776 autophagosome Cellular Component
GO:0005886 plasma membrane Cellular Component
GO:0012505 endomembrane system Cellular Component
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT3G58040
ath:AT3G61790
ath:AT4G27880
ath:AT5G53360
dosa:Os03g0356414
osa:9266295
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.

Cytoplasm0.582
Rank 1 · LXL04_011822 · OH-1004
Nucleus0.422
Rank 2 · LXL04_011822 · OH-1004
Cell membrane0.096
Rank 3 · LXL04_011822 · OH-1004
Mitochondrion0.077
Rank 4 · LXL04_011822 · OH-1004
Endoplasmic reticulum0.067
Rank 5 · LXL04_011822 · 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_RING50-85 aa
PF21361.4Sina_ZnF99-174 aa
PF03145.23Sina_TRAF194-291 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_011822PF21362.4Sina_RING50859.7e-1348.7
LXL04_011822PF21361.4Sina_ZnF991748e-29100.6
LXL04_011822PF03145.23Sina_TRAF1942912.4e-33115.2

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
Q84JL3Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT378.616%Swiss-Protstrong database homology
Q9STN8Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT476.415%Swiss-Protstrong database homology
Q8S3N1Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT585.393%Swiss-Protstrong database homology
Q9M2P4Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT272.054%Swiss-Protstrong database homology
Q10L91Oryza sativa subsp. japonicaE3 ubiquitin-protein ligase DIS177.778%Swiss-Protstrong database homology

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