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

TkA02G053110
Reference: TK1151 Chr: Chr02 Coordinates: 13863967-13866259 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2058 bp · TkA02G053110|TK1151|cDNA

ATGCACAAAAACCCACCATGCAAACCGCCTCCATGCCCTCCTCATCATTCTTGGAAAAATCCAAAGTCTTTTCATTTCCACAAGACTTGTCAACCTTTACGCCAATCTTGGAAACATCTCATTATCCCAACAAACCTTCGATCAAATCCAAAACAAAGATGTGTACACGTGGAACTCCATGGGTTGGAATGGGATGTGTATGTAGCTGCCTCTTTGGTTCACATGTATTGTCGTTTTGGGGGTTTTGATGCTGCTTATGG...

CDS

Download CDS FASTA

2058 bp · TkA02G053110|TK1151|CDS

ATGCACAAAAACCCACCATGCAAACCGCCTCCATGCCCTCCTCATCATTCTTGGAAAAATCCAAAGTCTTTTCATTTCCACAAGACTTGTCAACCTTTACGCCAATCTTGGAAACATCTCATTATCCCAACAAACCTTCGATCAAATCCAAAACAAAGATGTGTACACGTGGAACTCCATGGGTTGGAATGGGATGTGTATGTAGCTGCCTCTTTGGTTCACATGTATTGTCGTTTTGGGGGTTTTGATGCTGCTTATGG...

Protein

Download Protein FASTA

685 aa · TkA02G053110|TK1151|PROTEIN

MHKNPPCKPPPCPPHHSWKNPKSFHFHKTCQPLRQSWKHLIIPTNLRSNPKQRCVHVELHGLEWDVYVAASLVHMYCRFGGFDAAYGIFTNMPFRDMGCWNAIISGFCQNGKGEKALEILNEMKFEGIKLDSVTVATILPICAQMEDMIKGRLIHLFTELENSRKFFDDLPTRDLVSWNSIISGYEQNGNPNRALEFFHEMQKDGFTPDLLTLVSVASSIAQCGDTRGSKSVHGFVLRRYWFLKDVIIGNAVVDMYAKLG...

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 IDTkA02G053110
TK1151 IDTkA02G053110
OH-1004 IDLXL04_017317
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)92.600
Protein coverage (%)TK1151 93.577 / OH-1004 75.599
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 IDTkA02G053110
LocationChr02:13863967-13866259 (-)
DescriptionSimilar to EMB2758: Pentatricopeptide repeat-containing protein At4g33990
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g33990 Pentatricopeptide repeat-containing protein At4g33990. No verified direct reference in this release
At3g26782 Pentatricopeptide repeat-containing protein At3g26782, mitochondrial. No verified direct reference in this release
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
At4g30700 Pentatricopeptide repeat-containing protein At4g30700. No verified direct reference in this release
At3g57430 Involved in RNA editing events in chloroplasts.
A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_017317 · 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:0000963 mitochondrial RNA processing Biological Process
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0016556 mRNA modification Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0004519 endonuclease activity Molecular Function
KEGG gene cross-reference
ath:AT1G11290
ath:AT3G57430
ath:AT4G30700
ath:AT4G33990
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.

Mitochondrion0.621
Rank 1 · TkA02G053110 · TK1151
Plastid0.244
Rank 2 · TkA02G053110 · TK1151
Nucleus0.056
Rank 3 · TkA02G053110 · TK1151
Cytoplasm0.040
Rank 4 · TkA02G053110 · TK1151
Peroxisome0.007
Rank 5 · TkA02G053110 · 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.

PF13812PPR_358-92 aa
PF23276TPR_2458-93 aa
PF29070MSC6_N69-142 aa
PF13041PPR_271-94 aa
PF01535PPR71-92 aa
PF12854PPR_171-92 aa
PF13041PPR_296-140 aa
PF12854PPR_196-124 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA02G053110PF13812PPR_358921e-2796.7
TkA02G053110PF23276TPR_2458935.4e-1452.9
TkA02G053110PF29070MSC6_N691422.1e-1454.1
TkA02G053110PF13041PPR_271946.8e-64212.5
TkA02G053110PF01535PPR71924.4e-60196.5
TkA02G053110PF12854PPR_171921.4e-44150.2
TkA02G053110PF13041PPR_2961406.8e-64212.5
TkA02G053110PF12854PPR_1961241.4e-44150.2
TkA02G053110PF01535PPR991284.4e-60196.5
TkA02G053110PF17177PPR_long991453.2e-0833.9
TkA02G053110PF13812PPR_31001421e-2796.7
TkA02G053110PF23276TPR_241011625.4e-1452.9
TkA02G053110PF12921ATP131011235e-0523.9
TkA02G053110PF20431E_motif1131243.3e-1660.0
TkA02G053110PF19189Mtf21171470.1312.7
TkA02G053110PF12854PPR_11271381.4e-44150.2

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
O81767Arabidopsis thalianasp|O81767|PP348_ARATH Pentatricopeptide repeat-containing protein At4g3399055.700%Swiss-ProtHigh
Q9LW32Arabidopsis thalianasp|Q9LW32|PP258_ARATH Pentatricopeptide repeat-containing protein At3g26782, mitochondrial42.000%Swiss-ProtMedium
Q3E6Q1Arabidopsis thalianasp|Q3E6Q1|PPR32_ARATH Pentatricopeptide repeat-containing protein At1g11290, chloroplastic38.500%Swiss-ProtMedium
Q9SUH6Arabidopsis thalianasp|Q9SUH6|PP341_ARATH Pentatricopeptide repeat-containing protein At4g3070038.500%Swiss-ProtMedium
Q7Y211Arabidopsis thalianasp|Q7Y211|PP285_ARATH Pentatricopeptide repeat-containing protein At3g57430, chloroplastic36.400%Swiss-ProtMedium

JBrowse

View in Genome Browser