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

TkA06G177350
Reference: TK1151 Chr: Chr06 Coordinates: 46474893-46475942 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1050 bp · TkA06G177350|TK1151|cDNA

ATGGCAATGTCCGCCCTGATACGGCCACCACATTTCATTGCGCTTGAACATGACACTCTCAAACTCCTAAAATACTTAGCGGGAACTAGAAACCTTGAGCTCGGTAAAGTAATTCACGCCCGTTTGATTGTCTCTGATCAATCCTCTGAATATAATACACTCGAGACCAACGCGCTGATCGACCTTTACTCCAAATGTGCGGCACTGGGATCTGCACGCCAAGTGTTCGATAAAATGACCAAACGAGATGTAGTTTCCTG...

CDS

Download CDS FASTA

1050 bp · TkA06G177350|TK1151|CDS

ATGGCAATGTCCGCCCTGATACGGCCACCACATTTCATTGCGCTTGAACATGACACTCTCAAACTCCTAAAATACTTAGCGGGAACTAGAAACCTTGAGCTCGGTAAAGTAATTCACGCCCGTTTGATTGTCTCTGATCAATCCTCTGAATATAATACACTCGAGACCAACGCGCTGATCGACCTTTACTCCAAATGTGCGGCACTGGGATCTGCACGCCAAGTGTTCGATAAAATGACCAAACGAGATGTAGTTTCCTG...

Protein

Download Protein FASTA

349 aa · TkA06G177350|TK1151|PROTEIN

MAMSALIRPPHFIALEHDTLKLLKYLAGTRNLELGKVIHARLIVSDQSSEYNTLETNALIDLYSKCAALGSARQVFDKMTKRDVVSWSSLMAGLFQNGFSFEVLKSFNSMVSENDEFCQPNEYIFTLVLSSCSTLRYIQLGRQCHGYVLKSGLIFYEYVKNALVRLYSMMPDVVGAMEVLVSVPGYNTCTYNLILNGLIEHNYLHEASDIVKKMLTEQIMWDKSTYITIFTLCARLQDPYLGQQVHNKLLKSDIEFDVYV...

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 IDTkA06G177350
TK1151 IDTkA06G177350
OH-1004 IDLXL04_024107
Relationship / confidenceSequence Supported Annotation Or Model Conflict / Review
Protein identity (%)99.100
Protein coverage (%)TK1151 97.994 / OH-1004 49.138
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 IDTkA06G177350
LocationChr06:46474893-46475942 (+)
DescriptionSimilar to EMB2744: Pentatricopeptide repeat-containing protein At5g39680
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
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
At2g03380 Pentatricopeptide repeat-containing protein At2g03380, mitochondrial. No verified direct reference in this release
At4g13650 Pentatricopeptide repeat-containing protein At4g13650. No verified direct reference in this release
At3g14330 Pentatricopeptide repeat-containing protein At3g14330. No verified direct reference in this release
At3g22150 Pentatricopeptide repeat-containing protein At3g22150, chloroplastic. 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_024107 · 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:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing 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:AT2G27610
ath:AT4G30700
ath:AT5G39680
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.

Mitochondrion0.648
Rank 1 · TkA06G177350 · TK1151
Plastid0.203
Rank 2 · TkA06G177350 · TK1151
Nucleus0.040
Rank 3 · TkA06G177350 · TK1151
Cytoplasm0.032
Rank 4 · TkA06G177350 · TK1151
Cell membrane0.006
Rank 5 · TkA06G177350 · 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.

PF09098Dehyd-heme_bind18-92 aa
PF17049AEP137-85 aa
PF17867AAA_lid_743-108 aa
PF23276TPR_2444-85 aa
PF13812PPR_350-82 aa
PF13762MNE152-83 aa
PF13041PPR_257-84 aa
PF01535PPR57-83 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA06G177350PF09098Dehyd-heme_bind18920.1612.3
TkA06G177350PF17049AEP137850.03913.8
TkA06G177350PF17867AAA_lid_7431080.06114.3
TkA06G177350PF23276TPR_2444858.6e-0936.1
TkA06G177350PF13812PPR_350822.5e-1350.6
TkA06G177350PF13762MNE152830.1912.4
TkA06G177350PF13041PPR_257849.6e-34116.0
TkA06G177350PF01535PPR57831.7e-2691.3
TkA06G177350PF12854PPR_157803.8e-1556.0
TkA06G177350PF00637Clathrin57790.01515.8
TkA06G177350PF17177PPR_long60816.5e-0626.4
TkA06G177350PF13041PPR_2821329.6e-34116.0
TkA06G177350PF12854PPR_182983.8e-1556.0
TkA06G177350PF13812PPR_3831322.5e-1350.6
TkA06G177350PF17177PPR_long84846.5e-0626.4
TkA06G177350PF01535PPR851141.7e-2691.3

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
Q3E6Q1Arabidopsis thalianasp|Q3E6Q1|PPR32_ARATH Pentatricopeptide repeat-containing protein At1g11290, chloroplastic29.700%Swiss-ProtLow
Q9ZQ74Arabidopsis thalianasp|Q9ZQ74|PP146_ARATH Pentatricopeptide repeat-containing protein At2g03380, mitochondrial29.700%Swiss-ProtLow
Q9SVP7Arabidopsis thalianasp|Q9SVP7|PP307_ARATH Pentatricopeptide repeat-containing protein At4g1365030.300%Swiss-ProtMedium
Q9LUL5Arabidopsis thalianasp|Q9LUL5|PP229_ARATH Pentatricopeptide repeat-containing protein At3g1433029.200%Swiss-ProtLow
Q9LIE7Arabidopsis thalianasp|Q9LIE7|PP246_ARATH Pentatricopeptide repeat-containing protein At3g22150, chloroplastic29.100%Swiss-ProtLow

JBrowse

View in Genome Browser