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

TkA08G003580
Reference: TK1151 Chr: Chr08 Coordinates: 917190-922682 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2233 bp · TkA08G003580|TK1151|cDNA

GCTTATTATCTTCTGGATCACTTTTGTTTTCTTTGTTTGGTACAAATCTTTCCGGTGGGAAGAACCAAGCCTGATGGAATTCTGATCGCTGATCGTTTCTGTGTTGCGTTAATCTGCATTTCGTTCTCGATCACTTCTGTTTTCTTTCTTCGGTACAAATATTGCTCGTGTGAAGAACCAAACGCTTCTGTGTTGCATTAAGATGTGATTTCTTCTGTGCTACCTTCTGTTTCTGCTTCTTTATAGGTTCTTGATTTACT...

CDS

Download CDS FASTA

1533 bp · TkA08G003580|TK1151|CDS

ATGAAGCAGCTGAAAGAAATCCATGCCCACACCCTGCGCAATGGCATAGATTTCACCAAATTCCTTATCACGAAGCTCATTGAAATCCCAAACATCCCTTACGCTCACAGACTGTTGGACCTTATTCCTCAACCGACCGTCTTCCACTATAACAAACTGATTCAAGCTTTGTCCTGGCATGGCCCTCACCACAAATGTTTTGCGATTTACACCCGAATGCGCCTCAACGGTTGCTCCCCTAACCAGCACTCCTTCACTTC...

Protein

Download Protein FASTA

510 aa · TkA08G003580|TK1151|PROTEIN

MKQLKEIHAHTLRNGIDFTKFLITKLIEIPNIPYAHRLLDLIPQPTVFHYNKLIQALSWHGPHHKCFAIYTRMRLNGCSPNQHSFTSLFAASATLNSPTQAEIVHAHLVKSGYEFDLYASTALVDMYGKLGRLACARQVFDKMPSKDLPTWNSLIAGYARNGDMEGALEVFDEMPVKNVVSWTAMISGYSQNGEYGKSLKLFMEMEKKKDVHPNEVTIASALPACTSLGAVEVGQRIERYARGRGYLKNLFVCNALLEMY...

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 IDTkA08G003580
TK1151 IDTkA08G003580
OH-1004 IDLXL04_026632
Relationship / confidenceRbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)99.800
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 IDTkA08G003580
LocationChr08:917190-922682 (-)
DescriptionSimilar to PCMP-E20: Pentatricopeptide repeat-containing protein At5g08510
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g08510 Pentatricopeptide repeat-containing protein At5g08510. No verified direct reference in this release
At2g20540 Pentatricopeptide repeat-containing protein At2g20540. No verified direct reference in this release
At3g46790 Required for the intergenic processing between chloroplast rsp7 and ndhB transcripts. No verified direct reference in this release
At5g56310 Pentatricopeptide repeat-containing protein At5g56310. No verified direct reference in this release
At5g44230 Pentatricopeptide repeat-containing protein At5g44230. 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_026632 · 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:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0005576 extracellular region Cellular Component
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:AT2G20540
ath:AT4G37380
ath:AT5G08510
ath:AT5G44230
ath:AT5G56310
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.

Mitochondrion0.672
Rank 1 · TkA08G003580 · TK1151
Plastid0.167
Rank 2 · TkA08G003580 · TK1151
Nucleus0.063
Rank 3 · TkA08G003580 · TK1151
Cytoplasm0.031
Rank 4 · TkA08G003580 · TK1151
Cell membrane0.006
Rank 5 · TkA08G003580 · 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.

PF22330Rib_mS39_PPR35-59 aa
PF12854PPR_144-57 aa
PF13812PPR_344-89 aa
PF13041PPR_245-91 aa
PF23276TPR_2448-142 aa
PF01535PPR49-78 aa
PF03704BTAD50-74 aa
PF29070MSC6_N51-140 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA08G003580PF22330Rib_mS39_PPR35590.2411.9
TkA08G003580PF12854PPR_144571.7e-34117.9
TkA08G003580PF13812PPR_344895.4e-2588.0
TkA08G003580PF13041PPR_245918.3e-54180.2
TkA08G003580PF23276TPR_24481422.1e-1351.0
TkA08G003580PF01535PPR49788.2e-52170.6
TkA08G003580PF03704BTAD50740.113.7
TkA08G003580PF29070MSC6_N511403.7e-1143.5
TkA08G003580PF17177PPR_long641488.5e-1245.6
TkA08G003580PF12854PPR_176881.7e-34117.9
TkA08G003580PF13812PPR_31081445.4e-2588.0
TkA08G003580PF13041PPR_21211478.3e-54180.2
TkA08G003580PF01535PPR1211478.2e-52170.6
TkA08G003580PF12854PPR_11211431.7e-34117.9
TkA08G003580PF14559TPR_191211470.003118.5
TkA08G003580PF13428TPR_141221433.6e-0730.9

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
Q9FNN7Arabidopsis thalianasp|Q9FNN7|PP371_ARATH Pentatricopeptide repeat-containing protein At5g0851056.800%Swiss-ProtHigh
Q9SIL5Arabidopsis thalianasp|Q9SIL5|PP165_ARATH Pentatricopeptide repeat-containing protein At2g2054042.400%Swiss-ProtMedium
Q9STF3Arabidopsis thalianasp|Q9STF3|PP265_ARATH Pentatricopeptide repeat-containing protein CRR2, chloroplastic32.800%Swiss-ProtMedium
Q9FMA1Arabidopsis thalianasp|Q9FMA1|PP433_ARATH Pentatricopeptide repeat-containing protein At5g5631036.000%Swiss-ProtMedium
Q9FFG8Arabidopsis thalianasp|Q9FFG8|PP417_ARATH Pentatricopeptide repeat-containing protein At5g4423042.600%Swiss-ProtMedium

JBrowse

View in Genome Browser