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

TkA04G045660
Reference: TK1151 Chr: Chr04 Coordinates: 12316514-12320585 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2279 bp · TkA04G045660|TK1151|cDNA

GTTAAATGTTAGGTTAAGCTCTCACACAAAAAGCCAAAGCCTACCCCCCTCCCCTCTCCTTCTCTGTTCCTGCTCGTGACACCATCATCACACTCTATATTCTCTTTCATGGAGAGACTACCCTGACCCTGACCTCCTTCGGTCTCCGGTATCTGTCACTATCGATTTGGCACAATCTCGTCTATAATCGCTTAATTTCTTGAAAGTGGTTGGGAGGATTTTGTTTTAGATCTTTTGAGAATTTGGGAAGCTGTTGTTAT...

CDS

Download CDS FASTA

1941 bp · TkA04G045660|TK1151|CDS

ATGGCGGAAGGAGGGAAAGGTGGAGTGGTACTGAAGCTGATTGATATCGTGAGCGAGATATCGCTGATATCGGATTATAGGTGTACTGTGAGGAAGCCGTTTTTCAATTTAGCGCGAAGGTTGAAGCTTTTGAGTCCATTGTTTGAAGAGATTCGTGATATTAAAGACCCCCTACCTGATGATTCCTACCGATCGTTGCTTTCCTTAATGGAGGCTTTGGAATCTGCTAAAGAGTTGCTTCGATTAGGGAGTCAAGCCAG...

Protein

Download Protein FASTA

646 aa · TkA04G045660|TK1151|PROTEIN

MAEGGKGGVVLKLIDIVSEISLISDYRCTVRKPFFNLARRLKLLSPLFEEIRDIKDPLPDDSYRSLLSLMEALESAKELLRLGSQASKIYLALEREEIMKKYQEVTERLEQDLDGICFEKLDISDEVKEQVALVVAQFRRAKGKTDTPDPELTDDLSSLYNKGSDVASDPDVLKRLVEKLQLTGITDLTNESITLHEMVTASDGDPGETIEKMSMLLKRIKDFVQTDNTNTQQDSDSPTTDTSTSAPQNYRISLRNPKTT...

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 IDTkA04G045660
TK1151 IDTkA04G045660
OH-1004 IDLXL04_017790
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)78.800
Protein coverage (%)TK1151 98.916 / OH-1004 96.600
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 versionTK1151 / GWHBCHF00000000
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDTkA04G045660
LocationChr04:12316514-12320585 (-)
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
UniProt: A2ZLU6 Defense related protein that negatively regulates programmed cell death. No verified direct reference in this release
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
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_017790 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Cytoplasm0.583
Rank 1 · TkA04G045660 · TK1151
Nucleus0.329
Rank 2 · TkA04G045660 · TK1151
Cell membrane0.233
Rank 3 · TkA04G045660 · TK1151
Endoplasmic reticulum0.056
Rank 4 · TkA04G045660 · TK1151
Golgi apparatus0.052
Rank 5 · TkA04G045660 · TK1151

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.

PF25240PUB2_N29-105 aa
PF25368PUB10_N31-142 aa
PF22215MLKL_N36-111 aa
PF04826Arm_241-105 aa
PF30700ARM_GAC_1st65-123 aa
PF25598ARM_PUB74-95 aa
PF13639zf-RING_2116-128 aa
PF13513HEAT_EZ126-165 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G045660PF25240PUB2_N291050.0116.5
TkA04G045660PF25368PUB10_N311421.1e-36126.9
TkA04G045660PF22215MLKL_N361110.008216.4
TkA04G045660PF04826Arm_2411050.004517.2
TkA04G045660PF30700ARM_GAC_1st651230.199.6
TkA04G045660PF25598ARM_PUB74951.2e-2591.4
TkA04G045660PF13639zf-RING_21161280.04914.6
TkA04G045660PF13513HEAT_EZ1261650.4211.9
TkA04G045660PF25368PUB10_N2122581.1e-36126.9
TkA04G045660PF25598ARM_PUB2162241.2e-2591.4
TkA04G045660PF04564U-box2623323.9e-2382.1
TkA04G045660PF11789zf-Nse2653050.000221.8
TkA04G045660PF13923zf-C3HC4_22673050.002318.4
TkA04G045660PF13639zf-RING_22673040.04914.6
TkA04G045660PF13445zf-RING_UBOX2683043.2e-0524.5
TkA04G045660PF15227zf-C3HC4_42683040.0004920.9

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 thalianasp|Q9SNC6|PUB13_ARATH U-box domain-containing protein 1361.300%Swiss-ProtHigh
Q9ZV31Arabidopsis thalianasp|Q9ZV31|PUB12_ARATH U-box domain-containing protein 1251.500%Swiss-ProtMedium
Q8VZ40Arabidopsis thalianasp|Q8VZ40|PUB14_ARATH U-box domain-containing protein 1448.300%Swiss-ProtMedium
A2ZLU6Oryza sativa subsp. indicasp|A2ZLU6|SL11_ORYSI Protein spotted leaf 1155.600%Swiss-ProtMedium
Q0IMG9Oryza sativa subsp. japonicasp|Q0IMG9|SL11_ORYSJ E3 ubiquitin-protein ligase SPL1155.600%Swiss-ProtMedium

JBrowse

View in Genome Browser