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

TkA03G344380
Reference: TK1151 Chr: Chr03 Coordinates: 84712560-84714662 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2103 bp · TkA03G344380|TK1151|cDNA

ATGATCAGGTGTCATGGAATTGTCCTCAAACATAATTGCCTGTCATCCCTGATTTCAAGAAAATCGCTCAACACTCCGAAATGCTACTCCACTTTCCTTCTTCCACAAAATGACTGCACCACAAACAACACGACGACTATTCAAACATTCGCCGATTACGAGCGTGCCCTCGTCCAAGCATTGAAATCATCTTCTTCCCTTTCTGCACCGTTCCATTACGGCCAGCATCTCCATTGTCATATCTTCAAGGGCGGATATGA...

CDS

Download CDS FASTA

2103 bp · TkA03G344380|TK1151|CDS

ATGATCAGGTGTCATGGAATTGTCCTCAAACATAATTGCCTGTCATCCCTGATTTCAAGAAAATCGCTCAACACTCCGAAATGCTACTCCACTTTCCTTCTTCCACAAAATGACTGCACCACAAACAACACGACGACTATTCAAACATTCGCCGATTACGAGCGTGCCCTCGTCCAAGCATTGAAATCATCTTCTTCCCTTTCTGCACCGTTCCATTACGGCCAGCATCTCCATTGTCATATCTTCAAGGGCGGATATGA...

Protein

Download Protein FASTA

700 aa · TkA03G344380|TK1151|PROTEIN

MIRCHGIVLKHNCLSSLISRKSLNTPKCYSTFLLPQNDCTTNNTTTIQTFADYERALVQALKSSSSLSAPFHYGQHLHCHIFKGGYDSNIFIRNSLINFYAKSGAIHDAESIFVSGFQSDRISSNIMLAGYVNVGRLSDARHLFDKMPGKNSISFTTMIMGLARHGFWVEAIKLFKEMRSLGFVPTEVTMSSVLSSYSHISGIKTAQILHALVAKSGLEDFTLVLTSLVQLYCACSSLIDARILFDGMPERNIVSWNVML...

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 IDTkA03G344380
TK1151 IDTkA03G344380
OH-1004 IDLXL04_008696
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)99.900
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 IDTkA03G344380
LocationChr03:84712560-84714662 (+)
DescriptionSimilar to PCMP-E42: Pentatricopeptide repeat-containing protein At5g19020, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g19020 Pentatricopeptide repeat-containing protein At5g19020, mitochondrial. 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
At5g48910 Pentatricopeptide repeat-containing protein At5g48910. No verified direct reference in this release
At2g22410 Pentatricopeptide repeat-containing protein At2g22410, mitochondrial. No verified direct reference in this release
At1g08070 Involved in multiple sites RNA editing events in chloroplasts. 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_008696 · 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:0009451 RNA modification Biological Process
GO:0010182 sugar mediated signaling pathway 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:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G13600
ath:AT2G22070
ath:AT5G19020
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.

Mitochondrion0.598
Rank 1 · TkA03G344380 · TK1151
Plastid0.239
Rank 2 · TkA03G344380 · TK1151
Nucleus0.047
Rank 3 · TkA03G344380 · TK1151
Cytoplasm0.035
Rank 4 · TkA03G344380 · TK1151
Cell membrane0.005
Rank 5 · TkA03G344380 · 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.

PF00515TPR_152-57 aa
PF18768RNPP_C88-113 aa
PF13041PPR_289-113 aa
PF13812PPR_389-113 aa
PF01535PPR94-113 aa
PF12854PPR_194-113 aa
PF14559TPR_1996-113 aa
PF13812PPR_3116-147 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA03G344380PF00515TPR_152570.1812.4
TkA03G344380PF18768RNPP_C881130.2211.7
TkA03G344380PF13041PPR_2891137.4e-71234.8
TkA03G344380PF13812PPR_3891132.9e-1763.2
TkA03G344380PF01535PPR941131.6e-76248.1
TkA03G344380PF12854PPR_1941134.6e-44148.5
TkA03G344380PF14559TPR_19961132.8e-0834.7
TkA03G344380PF13812PPR_31161472.9e-1763.2
TkA03G344380PF12854PPR_11201474.6e-44148.5
TkA03G344380PF13041PPR_21221507.4e-71234.8
TkA03G344380PF01535PPR1231511.6e-76248.1
TkA03G344380PF14559TPR_191311492.8e-0834.7
TkA03G344380PF13432TPR_161321450.07114.3
TkA03G344380PF22330Rib_mS39_PPR1401660.001619.0
TkA03G344380PF13041PPR_21511977.4e-71234.8
TkA03G344380PF12854PPR_11511794.6e-44148.5

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
P0C8Q8Arabidopsis thalianasp|P0C8Q8|PP394_ARATH Pentatricopeptide repeat-containing protein At5g19020, mitochondrial52.800%Swiss-ProtHigh
Q7Y211Arabidopsis thalianasp|Q7Y211|PP285_ARATH Pentatricopeptide repeat-containing protein At3g57430, chloroplastic34.000%Swiss-ProtMedium
Q9FI80Arabidopsis thalianasp|Q9FI80|PP425_ARATH Pentatricopeptide repeat-containing protein At5g4891036.600%Swiss-ProtMedium
Q9SJZ3Arabidopsis thalianasp|Q9SJZ3|PP169_ARATH Pentatricopeptide repeat-containing protein At2g22410, mitochondrial34.500%Swiss-ProtMedium
Q9LN01Arabidopsis thalianasp|Q9LN01|PPR21_ARATH Pentatricopeptide repeat-containing protein At1g08070, chloroplastic36.100%Swiss-ProtMedium

JBrowse

View in Genome Browser