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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

TkA02G461220
Reference: TK1151 Chr: Chr02 Coordinates: 117505548-117512163 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3441 bp · TkA02G461220|TK1151|cDNA

ATGAAAAGAGACAAGTACGCTCCGCCTCCAAAACGAAAATCAGACAAAAACATTTTTCAAGAAAATGTAATGGATTTTGATCAGTTTGTGAGCGAGGGGTACAACTTTCTTGGAAACCATCTGATTTCTTGTATTGAAAGCTTGTACACACATATGCCTACATCTATCATTTCAGTCGAGGCAGCTAAAAAAATGAACGGACTTGTTAGTTCTCTTAAGCTTTTTGAAAGATTACTGAAACAGACAGTTAATTCAGATGC...

CDS

Download CDS FASTA

3441 bp · TkA02G461220|TK1151|CDS

ATGAAAAGAGACAAGTACGCTCCGCCTCCAAAACGAAAATCAGACAAAAACATTTTTCAAGAAAATGTAATGGATTTTGATCAGTTTGTGAGCGAGGGGTACAACTTTCTTGGAAACCATCTGATTTCTTGTATTGAAAGCTTGTACACACATATGCCTACATCTATCATTTCAGTCGAGGCAGCTAAAAAAATGAACGGACTTGTTAGTTCTCTTAAGCTTTTTGAAAGATTACTGAAACAGACAGTTAATTCAGATGC...

Protein

Download Protein FASTA

1146 aa · TkA02G461220|TK1151|PROTEIN

MKRDKYAPPPKRKSDKNIFQENVMDFDQFVSEGYNFLGNHLISCIESLYTHMPTSIISVEAAKKMNGLVSSLKLFERLLKQTVNSDAGLSEALKGFSDNSSLHACRITLRFPEFKKKYEVKRFCLANACLIFSTASSSINMHTNGAKPIEVIVIDEAAQLKECESLIPLQLKGVRHVVLVGDERQLPAMVQSKISEEAEFGRSLFERLVSLGHKKHLLNVQYRMHPSISQFPNKKFYDKQILDGVNVKRIDYEKRFLKGN...

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 IDTkA02G461220
TK1151 IDTkA02G461220
OH-1004 IDLXL04_022446
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)43.200
Protein coverage (%)TK1151 48.866 / OH-1004 20.739
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 IDTkA02G461220
LocationChr02:117505548-117512163 (-)
DescriptionSimilar to Trank1: TPR and ankyrin repeat-containing protein 1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g47010 Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons (premature termination codon PTC) by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery.
Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis.2009 · DOI: 10.1073/pnas.0808902106
Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense.2011 · DOI: 10.1093/pcp/pcr144
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.2012 · DOI: 10.1093/nar/gkr932
Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses.2012 · DOI: 10.1111/j.1744-7909.2012.01093.x

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_022446 · 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:0006283 transcription-coupled nucleotide-excision repair Biological Process
GO:0006353 DNA-templated transcription termination Biological Process
GO:0006357 regulation of transcription by RNA polymerase II Biological Process
GO:0006364 rRNA processing Biological Process
GO:0006369 termination of RNA polymerase II transcription Biological Process
GO:0006386 termination of RNA polymerase III transcription Biological Process
GO:0006399 tRNA metabolic process Biological Process
GO:0006974 DNA damage response Biological Process
GO:0008033 tRNA processing Biological Process
GO:0009553 embryo sac development Biological Process
GO:0009875 pollen-pistil interaction Biological Process
GO:0010183 pollen tube guidance Biological Process
KEGG gene cross-reference
ath:AT4G15570
hsa:9881
mmu:320429
sce:YLR430W
spo:2540523
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.

Cytoplasm0.539
Rank 1 · TkA02G461220 · TK1151
Nucleus0.398
Rank 2 · TkA02G461220 · TK1151
Mitochondrion0.079
Rank 3 · TkA02G461220 · TK1151
Cell membrane0.069
Rank 4 · TkA02G461220 · TK1151
Endoplasmic reticulum0.060
Rank 5 · TkA02G461220 · 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.

PF13086AAA_11113-193 aa
PF01443Viral_helicase1139-207 aa
PF13245AAA_19142-189 aa
PF13604AAA_30142-193 aa
PF13087AAA_12201-389 aa
PF01443Viral_helicase1323-388 aa
PF20073DUF6469663-879 aa
PF13086AAA_11889-943 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA02G461220PF13086AAA_111131932.7e-46159.2
TkA02G461220PF01443Viral_helicase11392073.4e-0834.3
TkA02G461220PF13245AAA_191421891.4e-0732.4
TkA02G461220PF13604AAA_301421931.2e-0629.1
TkA02G461220PF13087AAA_122013894e-61206.7
TkA02G461220PF01443Viral_helicase13233883.4e-0834.3
TkA02G461220PF20073DUF64696638794.4e-32112.0
TkA02G461220PF13086AAA_118899432.7e-46159.2
TkA02G461220PF13245AAA_1995511081.4e-0732.4
TkA02G461220PF13086AAA_11103911122.7e-46159.2
TkA02G461220PF13604AAA_30106111131.2e-0629.1
TkA02G461220PF01443Viral_helicase1106611253.4e-0834.3
TkA02G461220PF13087AAA_12112011454e-61206.7

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
Q9FJR0Arabidopsis thalianasp|Q9FJR0|RENT1_ARATH Regulator of nonsense transcripts 1 homolog39.400%Swiss-ProtLow

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