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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

TkA04G002940
Reference: TK1151 Chr: Chr04 Coordinates: 731911-735117 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2980 bp · TkA04G002940|TK1151|cDNA

GGGTGGATATTCCAATGTAGCACCACTCCAGCTCAGCTACAAGCCACTGCGTCTCTTCCTTTCTCTTTGCCTTTTGGTCTTTTTATCTACAATCTCTCTCAAACCCTACTCACCCCCCTTATCTTGTTGGTGATGGCGTCTTCCACACCACCAACCTTGACCACCACGAAATCATATCAGAACCACCATATACAAGGCCTACAGAACCATCACCGCCGTACACACAATGGTCATAACCCCCTCCATCCATCCCCAAAGGT...

CDS

Download CDS FASTA

2688 bp · TkA04G002940|TK1151|CDS

GGGTGGATATTCCAATGTAGCACCACTCCAGCTCAGCTACAAGCCACTGCGTCTCTTCCTTTCTCTTTGCCTTTTGGTCTTTTTATCTACAATCTCTCTCAAACCCTACTCACCCCCCTTATCTTGTTGGTGATGGCGTCTTCCACACCACCAACCTTGACCACCACGAAATCATATCAGAACCACCATATACAAGGCCTACAGAACCATCACCGCCGTACACACAATGGTCATAACCCCCTCCATCCATCCCCAAAGGT...

Protein

Download Protein FASTA

895 aa · TkA04G002940|TK1151|PROTEIN

GWIFQCSTTPAQLQATASLPFSLPFGLFIYNLSQTLLTPLILLVMASSTPPTLTTTKSYQNHHIQGLQNHHRRTHNGHNPLHPSPKVSLHPPAPRNPTANKPPIPAPTTVTAGASSSLQHRNSTFAPLSSKSELAADFSGRRSTRFVSKMHFGRPKAGGSSRHSVLAEDALQQLIRCSGDDRLVESVLLNFQSKLCGSDDYNFLLRELGNRNEWSMAIQCFEFAVSRERRRTEQGKLASSMISVLGRLGKIDLAKKVFET...

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 IDTkA04G002940
TK1151 IDTkA04G002940
OH-1004 IDLXL04_037103
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)100.000
Protein coverage (%)TK1151 100.000 / OH-1004 99.114
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 IDTkA04G002940
LocationChr04:731911-735117 (+)
DescriptionSimilar to At2g31400: Pentatricopeptide repeat-containing protein At2g31400, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g31400 Involved in nuclear gene expression via the retrograde plastid-to-nucleus signaling.
Signals from chloroplasts converge to regulate nuclear gene expression.2007 · PMID: 17395793
Plastid signals that affect photomorphogenesis in Arabidopsis thaliana are dependent on GENOMES UNCOUPLED 1 and cryptochrome 1.2009 · DOI: 10.1111/j.1469-8137.2008.02729.x
The Arabidopsis plastid-signalling mutant gun1 (genomes uncoupled1) shows altered sensitivity to sucrose and abscisic acid and alterations in early seedling development.2010 · DOI: 10.1093/jxb/erq186
Timing the switch to phototrophic growth: a possible role of GUN1.2011 · DOI: 10.4161/psb.6.4.14900

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_037103 · 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:0010019 chloroplast-nucleus signaling pathway Biological Process
GO:0031930 mitochondria-nucleus signaling pathway Biological Process
GO:0042793 plastid transcription Biological Process
GO:0045893 positive regulation of DNA-templated transcription Biological Process
GO:0009507 chloroplast Cellular Component
GO:0042644 chloroplast nucleoid Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G74850
ath:AT2G31400
ath:AT5G02860
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.

Plastid0.796
Rank 1 · TkA04G002940 · TK1151
Mitochondrion0.160
Rank 2 · TkA04G002940 · TK1151
Nucleus0.068
Rank 3 · TkA04G002940 · TK1151
Cytoplasm0.039
Rank 4 · TkA04G002940 · TK1151
Cell membrane0.015
Rank 5 · TkA04G002940 · 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.

PF06679DUF118068-137 aa
PF13424TPR_12168-193 aa
PF13041PPR_2201-222 aa
PF01535PPR201-222 aa
PF00515TPR_1210-226 aa
PF13176TPR_7211-222 aa
PF29070MSC6_N213-284 aa
PF12854PPR_1239-259 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G002940PF06679DUF1180681370.411.8
TkA04G002940PF13424TPR_121681930.0001222.9
TkA04G002940PF13041PPR_22012223.6e-91299.9
TkA04G002940PF01535PPR2012221.1e-71232.9
TkA04G002940PF00515TPR_12102262.1e-0524.8
TkA04G002940PF13176TPR_72112220.02215.5
TkA04G002940PF29070MSC6_N2132844.4e-2692.6
TkA04G002940PF12854PPR_12392591.9e-78258.5
TkA04G002940PF01535PPR2392611.1e-71232.9
TkA04G002940PF11848DUF33682392600.1113.3
TkA04G002940PF13041PPR_22402603.6e-91299.9
TkA04G002940PF13424TPR_122402940.0001222.9
TkA04G002940PF23276TPR_242423662.5e-31109.0
TkA04G002940PF13428TPR_142432763.9e-0524.6
TkA04G002940PF13181TPR_82442630.000919.9
TkA04G002940PF00515TPR_12452622.1e-0524.8

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
Q9SIC9Arabidopsis thalianasp|Q9SIC9|PP178_ARATH Pentatricopeptide repeat-containing protein GUN1, chloroplastic76.100%Swiss-ProtHigh

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