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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

TkA01G268630
Reference: TK1151 Chr: Chr01 Coordinates: 67381258-67388668 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1417 bp · TkA01G268630|TK1151|cDNA

ATCGCAACGGGAATTTGGAGTTGAATCAACATACAGTCTCGCCCGAGTCAACTCGTTACGTTTAACCCACCTATAACTTACAGCCCCTGTATCTTCCCCCTTCTGCCATTGTATCAAACCCTAGACAACATTATCGCAATTTTCTTTTATCATAATCACTTTCGTCTTCTAAGAAACCCCTGATTCCTCACCCCGATTTCTTTGATTTTCTTTAGAAAGCTATGGATTCTCAACCTAACAACTTATACGAAACGGCGTCT...

CDS

Download CDS FASTA

3744 bp · TkA01G268630|TK1151|CDS

ATGGATTCTCAACCTAACAACTTATACGAAACGGCGTCTCAGCCCGATACCGGCAACGATGACGCGTACACGTTCCTGGAATTCAACACGCAAGGCGAGGAAGACTTCAATTACCCGGACTTTCAAGAGCTCTCACAGCCCAATGCTGTTCGATCTTCACCGTCTTCATCAGTATGGCCCACACCATCCGACTCTATATCCGTCGACACCTCCGCCGCCGTCGACCACCGCTCTGACAGCAACGCCTCCCCTGGCTCAGC...

Protein

Download Protein FASTA

1247 aa · TkA01G268630|TK1151|PROTEIN

MDSQPNNLYETASQPDTGNDDAYTFLEFNTQGEEDFNYPDFQELSQPNAVRSSPSSSVWPTPSDSISVDTSAAVDHRSDSNASPGSATSGKGGGGRGNNNVNQTSAVDALAAGMSGLNFEETGDDESYEYGKGDFMEHACKYCGVQNPACVVRCNVPSCRKWFCNSRGNTSGSHIVNHLVRAKHKEVCLHKDSPLGETILECYNCGCRNVFLLGFISAKTESVVVLLCREPCLNVNALKDMNWDLSQWCPLIDDRCFLQW...

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 IDTkA01G268630
TK1151 IDTkA01G268630
OH-1004 IDLXL04_035456
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)34.600
Protein coverage (%)TK1151 33.039 / OH-1004 38.298
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 IDTkA01G268630
LocationChr01:67381258-67388668 (+)
DescriptionSimilar to IGHMBP2: DNA-binding protein SMUBP-2
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_035456 · 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:0000122 negative regulation of transcription by RNA polymerase II Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006412 translation Biological Process
GO:0006974 DNA damage response Biological Process
GO:1903459 mitotic DNA replication lagging strand elongation Biological Process
GO:0005634 nucleus Cellular Component
GO:0005654 nucleoplasm Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0005829 cytosol Cellular Component
GO:0016020 membrane Cellular Component
GO:0016604 nuclear body Cellular Component
GO:0033203 DNA helicase A complex Cellular Component
KEGG gene cross-reference
hsa:3508
maua:101836074
rno:29532
spo:2539412
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.

Cytoplasm0.552
Rank 1 · TkA01G268630 · TK1151
Nucleus0.522
Rank 2 · TkA01G268630 · TK1151
Mitochondrion0.065
Rank 3 · TkA01G268630 · TK1151
Cell membrane0.057
Rank 4 · TkA01G268630 · TK1151
Endoplasmic reticulum0.057
Rank 5 · TkA01G268630 · 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.

PF09416UPF1_Zn_bind138-291 aa
PF18141UPF1_1B_dom343-432 aa
PF13604AAA_30391-455 aa
PF13086AAA_11488-608 aa
PF13604AAA_30488-689 aa
PF04851ResIII488-558 aa
PF00580UvrD-helicase489-580 aa
PF02562PhoH490-545 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA01G268630PF09416UPF1_Zn_bind1382917.4e-73244.2
TkA01G268630PF18141UPF1_1B_dom3434324.3e-2794.7
TkA01G268630PF13604AAA_303914555.2e-1556.4
TkA01G268630PF13086AAA_114886083.2e-52178.6
TkA01G268630PF13604AAA_304886895.2e-1556.4
TkA01G268630PF04851ResIII4885583e-0628.0
TkA01G268630PF00580UvrD-helicase4895800.0004720.6
TkA01G268630PF02562PhoH4905450.006716.6
TkA01G268630PF00270DEAD4935580.0003421.1
TkA01G268630PF13245AAA_194956891.6e-1145.2
TkA01G268630PF20720nSTAND35005380.001519.0
TkA01G268630PF06745ATPase5025690.003317.5
TkA01G268630PF24883NPHP3_N5035420.001219.8
TkA01G268630PF13401AAA_225035520.03515.1
TkA01G268630PF13191AAA_165045940.01816.3
TkA01G268630PF13481AAA_255045330.1612.3

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
Q9FJR0Arabidopsis thalianasp|Q9FJR0|RENT1_ARATH Regulator of nonsense transcripts 1 homolog77.300%Swiss-ProtHigh

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