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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

TkA05G468580
Reference: TK1151 Chr: Chr05 Coordinates: 117370575-117375417 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3508 bp · TkA05G468580|TK1151|cDNA

AACGAAACGAAGAACATGGGTAGCTTCATGAGATAAACAAAAGCTAAAGAAAAACGAAAGAACATGGGTAGCTTCATGAGAAGCTAAAGAAAAACGAGGAAAAGGATAAAAGCTACATAACGAAACGAAGAAATATCGGAGACTTTAACTTGACTTCATTGCTAATTTACTATCCTTGATTCCTCTGTTTTTGTTCAAAACCCCTCCCTTTTGATTTTGCCTTTAATGTAAGGACAAACTTTAGAAAAGCAATCGCGAAT...

CDS

Download CDS FASTA

2850 bp · TkA05G468580|TK1151|CDS

ATGAAAGGAGGTTCTTCTGGAAAGAAAAAAGGAGCTTCCCGGAGTCAAGATCATGGCTTTGCAGAGTTGATCTTCTCATGGTCTTTCGACGACATAGTCAACGACGGCCTTTACGAACACCAGGTGGAGAAAATACCACTTACTTTCCAGTCTGAAGAACACTATTTCCGTTCTTTTGTTTATCCATTGCTAGAGGAAACACGTACTGAATTAGCTTCCACTATGAAGATGATGTACAGAGCTCCATTTGCAGATATTTC...

Protein

Download Protein FASTA

949 aa · TkA05G468580|TK1151|PROTEIN

MKGGSSGKKKGASRSQDHGFAELIFSWSFDDIVNDGLYEHQVEKIPLTFQSEEHYFRSFVYPLLEETRTELASTMKMMYRAPFADISSLRKAKGKEKLMYDVTVGDWRNSECRKELYRTLPGDLLILANGEPGSVSDLQSSKWAFLLVNNTEDDDGTPVQFKVTASQEIEIHDGMFVVFLMNITTQKRIWNSLHKHANLDIIKEILYPDSMVKEQCDECSLGCNNPIQRFDPSLVSKLNESQKAAIMAAIHKMECSHKSS...

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 IDTkA05G468580
TK1151 IDTkA05G468580
OH-1004 IDLXL04_022439
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)98.900
Protein coverage (%)TK1151 91.781 / OH-1004 91.781
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 IDTkA05G468580
LocationChr05:117370575-117375417 (-)
DescriptionSimilar to MAA3: Probable helicase MAGATAMA 3
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_022439 · 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:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process
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:0006397 mRNA processing 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
KEGG gene cross-reference
ath:AT4G15570
ddi:DDB_G0288923
sce:YLR430W
spo:2540523
spo:2541556
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.

Nucleus0.661
Rank 1 · TkA05G468580 · TK1151
Cytoplasm0.337
Rank 2 · TkA05G468580 · TK1151
Cell membrane0.049
Rank 3 · TkA05G468580 · TK1151
Endoplasmic reticulum0.037
Rank 4 · TkA05G468580 · TK1151
Mitochondrion0.036
Rank 5 · TkA05G468580 · 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.

PF20073DUF646917-213 aa
PF13086AAA_11237-440 aa
PF13604AAA_30238-303 aa
PF13245AAA_19258-600 aa
PF00004AAA264-282 aa
PF13401AAA_22264-286 aa
PF03831YjdM312-361 aa
PF19269Anticodon_2372-427 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA05G468580PF20073DUF6469172137.1e-70235.5
TkA05G468580PF13086AAA_112374403.1e-34119.6
TkA05G468580PF13604AAA_302383032.4e-0731.4
TkA05G468580PF13245AAA_192586002.6e-0938.1
TkA05G468580PF00004AAA2642820.02415.8
TkA05G468580PF13401AAA_222642860.1213.4
TkA05G468580PF03831YjdM3123610.00716.9
TkA05G468580PF19269Anticodon_23724270.1513.2
TkA05G468580PF13087AAA_123944353.1e-59200.5
TkA05G468580PF07346DUF14774024840.008717.0
TkA05G468580PF13086AAA_115296053.1e-34119.6
TkA05G468580PF13604AAA_305406032.4e-0731.4
TkA05G468580PF01443Viral_helicase15496030.000222.0
TkA05G468580PF13401AAA_225585730.1213.4
TkA05G468580PF13087AAA_126128083.1e-59200.5
TkA05G468580PF01443Viral_helicase17418050.000222.0

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 homolog33.200%Swiss-ProtLow

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