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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_022568
Reference: OH-1004 Chr: Chr05 Coordinates: 1671284-1672909 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

999 bp · LXL04_022568|LXL04_022568|OH1004|cDNA

ATGGAATACGATAGCATTGAATGCGTTTCAACCTCCGATGGATTGGGCACCAAAGAGATCCCACATCATCACCATTTCACGTCATCCAAAACTCACAACGTCAATGTTATTCCTTCAAAGCTTCATCCCACCAGTGTCCATGAACTCCTTGAATGCCCCGTATGTACAAACTCAATGTACCCTCCGATTCACCAGTGTCACAATGGGCACACGCTATGTTCAACATGTAAAACACTTGTGAACAACAAGTGTCCAACTTG...

CDS

Download CDS FASTA

999 bp · LXL04_022568|LXL04_022568|OH1004|CDS

ATGGAATACGATAGCATTGAATGCGTTTCAACCTCCGATGGATTGGGCACCAAAGAGATCCCACATCATCACCATTTCACGTCATCCAAAACTCACAACGTCAATGTTATTCCTTCAAAGCTTCATCCCACCAGTGTCCATGAACTCCTTGAATGCCCCGTATGTACAAACTCAATGTACCCTCCGATTCACCAGTGTCACAATGGGCACACGCTATGTTCAACATGTAAAACACTTGTGAACAACAAGTGTCCAACTTG...

Protein

Download Protein FASTA

332 aa · LXL04_022568|LXL04_022568|OH1004|PROTEIN

MEYDSIECVSTSDGLGTKEIPHHHHFTSSKTHNVNVIPSKLHPTSVHELLECPVCTNSMYPPIHQCHNGHTLCSTCKTLVNNKCPTCRQELGDIRCLALEKVAESLEFPCKYFQLGCPEIFPYYTKLKHELICNLRPYSCPYAGSECSVVGDIPFLVTHLRDDHKVDMHSGCTFNHRYVKSNPREVENATWMLTVFNCFGQYFCLHFEAFQLSMAPVYMAFVRFMGDEQDARNYSYSLEVGGNGRKLIWEGTPRSIRDGH...

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_022568
TK1151 IDTkA06G476020
OH-1004 IDLXL04_022568
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)99.700
Protein coverage (%)TK1151 98.408 / OH-1004 93.072
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_022568
LocationChr05:1671284-1672909 (+)
DescriptionSimilar to SINAT4: E3 ubiquitin-protein ligase SINAT4
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
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
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
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_022568 · 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.

Cytoplasm0.537
Rank 1 · LXL04_022568 · OH-1004
Nucleus0.426
Rank 2 · LXL04_022568 · OH-1004
Cell membrane0.098
Rank 3 · LXL04_022568 · OH-1004
Endoplasmic reticulum0.079
Rank 4 · LXL04_022568 · OH-1004
Mitochondrion0.061
Rank 5 · LXL04_022568 · 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_RING52-87 aa
PF21361.4Sina_ZnF101-176 aa
PF03145.23Sina_TRAF196-293 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_022568PF21362.4Sina_RING52873.4e-1350.2
LXL04_022568PF21361.4Sina_ZnF1011764.2e-29101.5
LXL04_022568PF03145.23Sina_TRAF1962933.8e-36124.2

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
Q9STN8Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT476.636%Swiss-Protstrong database homology
Q84JL3Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT377.918%Swiss-Protstrong database homology
Q8S3N1Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT581.849%Swiss-Protstrong database homology
Q9M2P4Arabidopsis thalianaE3 ubiquitin-protein ligase SINAT280.078%Swiss-Protstrong database homology
Q10L91Oryza sativa subsp. japonicaE3 ubiquitin-protein ligase DIS180.153%Swiss-Protstrong database homology

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