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

TkA03G398490
Reference: TK1151 Chr: Chr03 Coordinates: 99048104-99048970 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

834 bp · TkA03G398490|TK1151|cDNA

ATGAGCAGTTACCATGATTCGAATGTGATAGAGCTCGCCGGAAAAATCTTGATTGTGTCTATCGTAGTATTGTCCGTAGTTTTGATATTTGTTTTTTTTGTTCACCTCTACGCCAAGTGGTTCTGGCAGCGCCGTCGCCGTCGTCGGGGAGATTTTACAGCGGGTCACCAGGAACAACAGTCCGGCGTCACCGTTCTCCGGCGTGGGCTAAACCCCTCATTCCTGAAAACAATACCGGTTTTACCGTTCGACCGGAAAGA...

CDS

Download CDS FASTA

834 bp · TkA03G398490|TK1151|CDS

ATGAGCAGTTACCATGATTCGAATGTGATAGAGCTCGCCGGAAAAATCTTGATTGTGTCTATCGTAGTATTGTCCGTAGTTTTGATATTTGTTTTTTTTGTTCACCTCTACGCCAAGTGGTTCTGGCAGCGCCGTCGCCGTCGTCGGGGAGATTTTACAGCGGGTCACCAGGAACAACAGTCCGGCGTCACCGTTCTCCGGCGTGGGCTAAACCCCTCATTCCTGAAAACAATACCGGTTTTACCGTTCGACCGGAAAGA...

Protein

Download Protein FASTA

277 aa · TkA03G398490|TK1151|PROTEIN

MSSYHDSNVIELAGKILIVSIVVLSVVLIFVFFVHLYAKWFWQRRRRRRGDFTAGHQEQQSGVTVLRRGLNPSFLKTIPVLPFDRKDFKDGLECAVCLSELDEGEKTRILPKCSHGFHVECIDMWFHSHSTCPICRSSVSDQIEISVEDLLEIRQTQEESPENGDSHNFPTNILFWGDETEVSTLTSQLEEANNHHQTPVSASEPSSSTSSHAINDQSRPDLVIDIPRQIDDDEDQKSPVSYRMRSLRRILSGSRRFISP...

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 IDTkA03G398490
TK1151 IDTkA03G398490
OH-1004 IDLXL04_009102
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)92.400
Protein coverage (%)TK1151 100.000 / OH-1004 100.000
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 IDTkA03G398490
LocationChr03:99048104-99048970 (-)
DescriptionSimilar to ATL3: RING-H2 finger protein ATL3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g53820 RING-H2 finger protein ATL60. No verified direct reference in this release
At1g72310 RING-H2 finger protein ATL3. No verified direct reference in this release
At3g16720 May be involved in the early steps of the plant defense signaling pathway. No verified direct reference in this release
At3g62690 RING-H2 finger protein ATL5. No verified direct reference in this release
At2g47560 RING-H2 finger protein ATL64. 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_009102 · 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:0016567 protein ubiquitination Biological Process
GO:0042631 cellular response to water deprivation Biological Process
GO:0065003 protein-containing complex assembly Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0005886 plasma membrane Cellular Component
GO:0016020 membrane Cellular Component
GO:0008270 zinc ion binding Molecular Function
GO:0061630 ubiquitin protein ligase activity Molecular Function
GO:0061659 ubiquitin-like protein ligase activity Molecular Function
KEGG gene cross-reference
ath:AT1G53820
ath:AT1G72310
ath:AT3G14320
ath:AT3G16720
ath:AT3G62690
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.

Cell membrane0.290
Rank 1 · TkA03G398490 · TK1151
Cytoplasm0.263
Rank 2 · TkA03G398490 · TK1151
Nucleus0.206
Rank 3 · TkA03G398490 · TK1151
Endoplasmic reticulum0.205
Rank 4 · TkA03G398490 · TK1151
Lysosome / Vacuole0.198
Rank 5 · TkA03G398490 · 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.

PF12861zf-ANAPC1131-44 aa
PF14446Prok-RING_191-122 aa
PF13920zf-C3HC4_392-140 aa
PF11793FANCL_C92-131 aa
PF13639zf-RING_293-136 aa
PF17123zf-RING_1193-122 aa
PF13923zf-C3HC4_293-135 aa
PF14634zf-RING_593-136 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA03G398490PF12861zf-ANAPC1131448.1e-0523.3
TkA03G398490PF14446Prok-RING_1911220.07813.9
TkA03G398490PF13920zf-C3HC4_3921407.1e-0523.2
TkA03G398490PF11793FANCL_C921310.2312.5
TkA03G398490PF13639zf-RING_2931362.3e-1454.1
TkA03G398490PF17123zf-RING_11931225.5e-1142.7
TkA03G398490PF13923zf-C3HC4_2931352.6e-0731.1
TkA03G398490PF14634zf-RING_5931360.0001222.7
TkA03G398490PF17120zf-RING_16931330.06913.5
TkA03G398490PF21202SLX1_C931370.4111.7
TkA03G398490PF29452FAR1_N931380.4111.4
TkA03G398490PF03660PHF5931181.010.4
TkA03G398490PF12678zf-rbx1941369.6e-0832.9
TkA03G398490PF00097zf-C3HC4941358.9e-0523.0
TkA03G398490PF13445zf-RING_UBOX941330.0006820.3
TkA03G398490PF14447Prok-RING_4941430.01216.2

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
P0C035Arabidopsis thalianasp|P0C035|ATL60_ARATH RING-H2 finger protein ATL6035.900%Swiss-ProtMedium
Q9XF63Arabidopsis thalianasp|Q9XF63|ATL3_ARATH RING-H2 finger protein ATL331.600%Swiss-ProtMedium
Q8L9T5Arabidopsis thalianasp|Q8L9T5|ATL2_ARATH RING-H2 finger protein ATL246.000%Swiss-ProtLow
Q9LZJ6Arabidopsis thalianasp|Q9LZJ6|ATL5_ARATH RING-H2 finger protein ATL538.900%Swiss-ProtLow
O22255Arabidopsis thalianasp|O22255|ATL64_ARATH RING-H2 finger protein ATL6438.200%Swiss-ProtMedium

JBrowse

View in Genome Browser