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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

TkA06G108740
Reference: TK1151 Chr: Chr06 Coordinates: 28631277-28635974 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3608 bp · TkA06G108740|TK1151|cDNA

AAAACCGAAAGTCGCTTAATTTGGAAATTCACTAGATTTTTCATGATATTATGGAGGGCCACAATCCTTTCTTCTTTCTCGTTTAATCTGCTTAATTTCCTCAGTCCTAAACCAAGCACTCGAAGAAATGGCGAACACAAGCAACAGTTGGACTTTCAAGGAGTCGCAAAACAGAAAACGAGGCCTTTTAGACGTCGTCCTCTCGTGGTCTTTATCTGATATACTCAACAAAGATCTTTACAAGTTTCAGGTGAAAGAAA...

CDS

Download CDS FASTA

3099 bp · TkA06G108740|TK1151|CDS

ATGGCGAACACAAGCAACAGTTGGACTTTCAAGGAGTCGCAAAACAGAAAACGAGGCCTTTTAGACGTCGTCCTCTCGTGGTCTTTATCTGATATACTCAACAAAGATCTTTACAAGTTTCAGGTGAAAGAAATTCCGTTGACGTTCTCATCTACAATTGACTACATTGATTCATTCATTTATCCACTTCTCGAGGAAACACATGCAGATTTGCTCTCCCATGTTGCCGGAATCTCTCAGGCACCGGCAAGCCGTATTTC...

Protein

Download Protein FASTA

1032 aa · TkA06G108740|TK1151|PROTEIN

MANTSNSWTFKESQNRKRGLLDVVLSWSLSDILNKDLYKFQVKEIPLTFSSTIDYIDSFIYPLLEETHADLLSHVAGISQAPASRISVLQRIQTGKVTDLLYRIIITGTNYEPHVGDLIALTQVKPKCINDLDRPNSRFIIAYVTKITNQNPITLHVLSSDLIESNNQRETKEPSKTFAVHMTNLTTNMRIWAALNWQGNMNIIQRTLTSSSSPVGGKCKESCCEGGKEVIDSELRPTFESFNLDSSQEAAVLSCLATSR...

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 IDTkA06G108740
TK1151 IDTkA06G108740
OH-1004 IDLXL04_022441
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)38.600
Protein coverage (%)TK1151 96.415 / OH-1004 32.219
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 IDTkA06G108740
LocationChr06:28631277-28635974 (+)
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
At4g15570 Probable helicase that may regulate RNA molecules involved in nucleolar organization and pollen tube guidance.
Attractive and repulsive interactions between female and male gametophytes in Arabidopsis pollen tube guidance.2000 · DOI: 10.1242/dev.127.20.4511
MAA3 (MAGATAMA3) helicase gene is required for female gametophyte development and pollen tube guidance in Arabidopsis thaliana.2008 · DOI: 10.1093/pcp/pcn130
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_022441 · 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.

Nucleus0.506
Rank 1 · TkA06G108740 · TK1151
Cytoplasm0.471
Rank 2 · TkA06G108740 · TK1151
Cell membrane0.055
Rank 3 · TkA06G108740 · TK1151
Endoplasmic reticulum0.047
Rank 4 · TkA06G108740 · TK1151
Mitochondrion0.040
Rank 5 · TkA06G108740 · 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.

PF20073DUF646919-212 aa
PF00580UvrD-helicase151-196 aa
PF13086AAA_11243-606 aa
PF04851ResIII243-303 aa
PF13604AAA_30245-308 aa
PF20720nSTAND3260-296 aa
PF13191AAA_16261-304 aa
PF13245AAA_19265-310 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA06G108740PF20073DUF6469192125.2e-35121.6
TkA06G108740PF00580UvrD-helicase1511960.0003321.2
TkA06G108740PF13086AAA_112436061.1e-36127.7
TkA06G108740PF04851ResIII2433030.001219.5
TkA06G108740PF13604AAA_302453083.3e-0731.0
TkA06G108740PF20720nSTAND32602960.004917.3
TkA06G108740PF13191AAA_162613040.07614.2
TkA06G108740PF13245AAA_192653103.7e-0834.3
TkA06G108740PF01637ATPase_22652890.01915.5
TkA06G108740PF00580UvrD-helicase2685980.0003321.2
TkA06G108740PF07652Flavi_DEAD2683090.1512.8
TkA06G108740PF13401AAA_222692970.07114.1
TkA06G108740PF00004AAA2692850.2612.4
TkA06G108740PF01443Viral_helicase12702892.4e-0525.0
TkA06G108740PF28652SUV2_N2993200.0814.1
TkA06G108740PF01637ATPase_23543950.01915.5

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
B6SFA4Arabidopsis thalianasp|B6SFA4|MAA3_ARATH Probable helicase MAGATAMA 334.600%Swiss-ProtLow
Q9FJR0Arabidopsis thalianasp|Q9FJR0|RENT1_ARATH Regulator of nonsense transcripts 1 homolog35.500%Swiss-ProtLow

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