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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

TkA03G478810
Reference: TK1151 Chr: Chr03 Coordinates: 119692075-119700648 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

4750 bp · TkA03G478810|TK1151|cDNA

GATCAACTGTAAATAAGAGGTTTCCCATTTTGTTCACTCCATGCCTTCAACGTGTTAAATTGCTCCTTTTTAACCCTTTATCAATCTCTGCCCTATTCTTAAACAAAGTTTACTCGAATCGACCAAACAAGAAGCAAACTTGAAAAACGCTTTACCATTCGGTTTAACAATGGTTTAATCAAACCCGCTTGAATTTGAATATTCGAATCGAAAATCCAGTCAATTTGATACAAAAATTGAGAATTTTACGGCATAGAAGC...

CDS

Download CDS FASTA

3783 bp · TkA03G478810|TK1151|CDS

ATGCCTCGAACTGTTGTAGTACCTGCATGGGAATTGCCTTTCAGACGTCCCCAACATTCATCAGACCTCCAGAAATGGGAACCCGCATCCGTGCAGGTTGATGTGTCTGAACTGATGGTGGAGGCGGAGAATTCTATTGGAGTGAGGATTAGTGGACCTCCAAAGGATTTTGTGAAGGGAAGTATTAACAACCGTCCTTTTCGTCCTGGTGGTTTGGATGATTCCCAGTCCATAGGAAGGAGTCTTCCGGAAGGTTCTTG...

Protein

Download Protein FASTA

1260 aa · TkA03G478810|TK1151|PROTEIN

MPRTVVVPAWELPFRRPQHSSDLQKWEPASVQVDVSELMVEAENSIGVRISGPPKDFVKGSINNRPFRPGGLDDSQSIGRSLPEGSCNGEWVREVLDGAPAQVIPPSCKEGMNLGDLKGHPCSWIIHEDKRVPKTTSETTLSVQFDDLFKKAWEEDVTEVPIDGDTPELEINVIELDSPKSVPLEDENKSDVHNDSVVTESSVIDQILSTRSDGLSKGLDDSDSGDGGRQQPEEAKVWAVTGGSEGIADNFNELVPDMAL...

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.

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ID Mapping

Input IDTkA03G478810
TK1151 IDTkA03G478810
OH-1004 IDLXL04_009854
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)59.600
Protein coverage (%)TK1151 100.000 / OH-1004 95.490
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 IDTkA03G478810
LocationChr03:119692075-119700648 (+)
DescriptionSimilar to SKI2: DExH-box ATP-dependent RNA helicase DExH11
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g46960 Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).
A DExD/H box RNA helicase is important for K+ deprivation responses and tolerance in Arabidopsis thaliana.2011 · DOI: 10.1111/j.1742-4658.2011.08147.x
Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover.2012 · DOI: 10.1371/journal.pgen.1002652

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_009854 · 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:0000292 RNA fragment catabolic process Biological Process
GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006402 mRNA catabolic process Biological Process
GO:0006417 regulation of translation Biological Process
GO:0006813 potassium ion transport Biological Process
GO:0016441 post-transcriptional gene silencing Biological Process
GO:0030968 endoplasmic reticulum unfolded protein response Biological Process
GO:0035864 response to potassium ion Biological Process
GO:0051607 defense response to virus Biological Process
GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Biological Process
GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop decay Biological Process
KEGG gene cross-reference
ath:AT3G46960
sce:YLR398C
spo:2538841
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.

Nucleus0.516
Rank 1 · TkA03G478810 · TK1151
Cytoplasm0.424
Rank 2 · TkA03G478810 · TK1151
Mitochondrion0.099
Rank 3 · TkA03G478810 · TK1151
Cell membrane0.050
Rank 4 · TkA03G478810 · TK1151
Endoplasmic reticulum0.040
Rank 5 · TkA03G478810 · 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.

PF17911Ski2_N44-78 aa
PF17911Ski2_N205-225 aa
PF00270DEAD269-416 aa
PF13191AAA_16280-336 aa
PF22527DEXQc_Suv3288-398 aa
PF00271Helicase_C563-584 aa
PF00271Helicase_C627-703 aa
PF21408MTR4-like_stalk758-818 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA03G478810PF17911Ski2_N44780.0001222.6
TkA03G478810PF17911Ski2_N2052250.0001222.6
TkA03G478810PF00270DEAD2694162.2e-2383.5
TkA03G478810PF13191AAA_162803360.212.9
TkA03G478810PF22527DEXQc_Suv32883981.8e-0525.0
TkA03G478810PF00271Helicase_C5635842.1e-0628.7
TkA03G478810PF00271Helicase_C6277032.1e-0628.7
TkA03G478810PF21408MTR4-like_stalk7588181.3e-1248.5
TkA03G478810PF13234MTR4_beta-barrel7697842.2e-30107.1
TkA03G478810PF13234MTR4_beta-barrel82510562.2e-30107.1
TkA03G478810PF00336DNA_pol_viral_C9289780.1811.9
TkA03G478810PF21408MTR4-like_stalk99610211.3e-1248.5
TkA03G478810PF13191AAA_16107311290.212.9
TkA03G478810PF08148DSHCT108212522.3e-59200.7
TkA03G478810PF21408MTR4-like_stalk122112451.3e-1248.5

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
F4JAA5Arabidopsis thalianasp|F4JAA5|SKI2_ARATH DExH-box ATP-dependent RNA helicase DExH1168.100%Swiss-ProtHigh

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