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

TkA01G598790
Reference: TK1151 Chr: Chr01 Coordinates: 150810640-150813857 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2350 bp · TkA01G598790|TK1151|cDNA

CTCAGCCTAAACTCTAAACAAACTTACCCATAAACCATCCACTTGCATGAGTTGGGCCTTTTGGTACTCATGGGTTCCACATTCGGCCCATTCATAACTGGTTGCGCGATCCTTTTTAGAACACGGCGCCGGAAACTTGCGTCCAAATGCGTCCCGAATAATGGCCGATAACATGCCACGTCGTCTCCCGCCAGTTCATCAAATGTTTAAGTTACCCCTACCATTGACACCCAACCATCTTGTCACAGGGTTAGATTTGT...

CDS

Download CDS FASTA

1695 bp · TkA01G598790|TK1151|CDS

ATGCCGGCTCGAGCAAGACGAACGTTGTTCCCGGAGGTAGTTATTGAGAGGGACTCTGACACCGAGAAAAGTTCAGACGATGAAGAAGAGGTAGAAGACGACGTCGTTGAGTCAGATGATCAAGAAGAAGACGAAGTAGAGGTCGATGCGCGAAAAGTTAAAGAGGCTGAAGTTTCGTCTCCAGCCAATAAGAAGGGGAAGGCGCATATTACTATCAGTCTTAAGAAAGTCTGCAAGGTCTGTAAGAGAACGGGTCATCA...

Protein

Download Protein FASTA

564 aa · TkA01G598790|TK1151|PROTEIN

MPARARRTLFPEVVIERDSDTEKSSDDEEEVEDDVVESDDQEEDEVEVDARKVKEAEVSSPANKKGKAHITISLKKVCKVCKRTGHQAGFQGPTYIDCPMKPCFLCKLPGHTTVDCPHRAAMEFGVIPASRKRTNNSLDYVFERQVRHRVPSIKPEFVIPDEVNCAVIRYHSRRVTCLEFHPTNNNILLSGDKKGQLGVWDFGKVHEKTVYSNIHTCLLNNMKFSPANDGTVYAASSDGTMSSTDLETGLSTPLLDLNPN...

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 IDTkA01G598790
TK1151 IDTkA01G598790
OH-1004 IDLXL04_000625
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)100.000
Protein coverage (%)TK1151 92.730 / OH-1004 92.730
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 IDTkA01G598790
LocationChr01:150810640-150813857 (-)
DescriptionSimilar to DDB2: Protein DAMAGED DNA-BINDING 2
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g58760 May function as the substrate recognition module for a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex including DDB1A and CUL4 (By similarity).
Regulation and role of Arabidopsis CUL4-DDB1A-DDB2 in maintaining genome integrity upon UV stress.2008 · DOI: 10.1371/journal.pgen.1000093
The DDB1a interacting proteins ATCSA-1 and DDB2 are critical factors for UV-B tolerance and genomic integrity in Arabidopsis thaliana.2010 · DOI: 10.1111/j.1365-313x.2010.04157.x

Rice

Reference gene IDPossible functionPapers / DOI
Os01g0141700 Required for DNA repair.
Rice UV-damaged DNA binding protein homologues are most abundant in proliferating tissues.2003 · DOI: 10.1016/s0378-1119(03)00447-5
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_000625 · 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:0000209 protein polyubiquitination Biological Process
GO:0006281 DNA repair Biological Process
GO:0006289 nucleotide-excision repair Biological Process
GO:0009411 response to UV Biological Process
GO:0010224 response to UV-B Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0034644 cellular response to UV Biological Process
GO:0051865 protein autoubiquitination Biological Process
GO:0070914 UV-damage excision repair Biological Process
GO:0005634 nucleus Cellular Component
GO:0005654 nucleoplasm Cellular Component
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex Cellular Component
KEGG gene cross-reference
ath:AT5G58760
bta:519357
dosa:Os01g0141700
gga:423185
osa:4325482
xtr:493565
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.

Nucleus0.869
Rank 1 · TkA01G598790 · TK1151
Cytoplasm0.193
Rank 2 · TkA01G598790 · TK1151
Cell membrane0.031
Rank 3 · TkA01G598790 · TK1151
Mitochondrion0.022
Rank 4 · TkA01G598790 · TK1151
Endoplasmic reticulum0.017
Rank 5 · TkA01G598790 · 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.

PF09026CENP-B_dimeris16-50 aa
PF05764YL117-69 aa
PF05642Sporozoite_P6718-79 aa
PF14812PBP1_TM24-55 aa
PF14392zf-CCHC_474-89 aa
PF27939DUF836376-123 aa
PF00098zf-CCHC77-88 aa
PF29037DSE1_N102-251 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA01G598790PF09026CENP-B_dimeris16500.009517.1
TkA01G598790PF05764YL117696.07.6
TkA01G598790PF05642Sporozoite_P6718799.94.8
TkA01G598790PF14812PBP1_TM24550.06714.2
TkA01G598790PF14392zf-CCHC_474891.29.5
TkA01G598790PF27939DUF8363761230.02415.2
TkA01G598790PF00098zf-CCHC77880.01316.2
TkA01G598790PF29037DSE1_N1022511.3e-0835.0
TkA01G598790PF00098zf-CCHC1021180.01316.2
TkA01G598790PF14392zf-CCHC_41031171.29.5
TkA01G598790PF24805EIF3I1472476e-0523.0
TkA01G598790PF23215WD_LRWD11632061.9e-0524.6
TkA01G598790PF23419WD40_RFWD31632480.007416.4
TkA01G598790PF25047Beta-prop_TEP1_2nd1642484.4e-0833.3
TkA01G598790PF24814WD40_Prp191652492.6e-1557.0
TkA01G598790PF24105Beta-prop_CAF1B_HIR11652462e-0524.5

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
Q6NQ88Arabidopsis thalianasp|Q6NQ88|DDB2_ARATH Protein DAMAGED DNA-BINDING 267.300%Swiss-ProtHigh
Q84KJ3Oryza sativa subsp. japonicasp|Q84KJ3|DDB2_ORYSJ DNA damage-binding protein 268.500%Swiss-ProtHigh

JBrowse

View in Genome Browser