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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

TkA03G010560
Reference: TK1151 Chr: Chr03 Coordinates: 2666220-2672541 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3107 bp · TkA03G010560|TK1151|cDNA

ATTCTTAATTGACCTATTTCTATTAAACAATTTCACCCTAAACTACACCGCTATAAATAAATATCTCCTCCTTCCCACATTCTTCCCTTACGCTTCTCCTCCCTTCGAAGCGTGTTTTCCTCTCTACCCGCCTCGTATTTTCATACATCTACGAGAGAGGAAAATCTTCGCAGAAAAGGAGGTTTGTATCTTCTAATCCTAACCTAATCATCCACCGATTTAGCCGTTTCTATCCCTACGATTTCAGTGAGATTCATCTG...

CDS

Download CDS FASTA

1773 bp · TkA03G010560|TK1151|CDS

ATGGGTGCTGCAACTGAAGCTACTCCAGCTCCCCGTTATGCCCCAGATGACCCCAACCTTCCAAAACCATGGAAAGGGTTAGTTGATGGAACAACCGGCTACCTCTACTATTGGAATCCAGTCACCAATGTTACCCAATATGAAAAGCCCTCAGGTTCTAAAAGTTCAGATCAACAAAAGTCATCTTCAGTAGCCATAAGCTCTTCTGTTCAGTCTTCACAAAAAGAAAACCGTGTCATTGATGATGATGATGATAGATA...

Protein

Download Protein FASTA

590 aa · TkA03G010560|TK1151|PROTEIN

MGAATEATPAPRYAPDDPNLPKPWKGLVDGTTGYLYYWNPVTNVTQYEKPSGSKSSDQQKSSSVAISSSVQSSQKENRVIDDDDDRYGKTSNGGSKFSSRGHESTRSGSYNSHNAPNGAVAAGPGGSGLSPDAYRKRHEITVTGDNVPPPFTSFEDTGFPSELLREVLEAGFAAPTPIQAQSWPVALQSRDIVAIAKTGSGKTLGYLVPGFIHLKRVLKNRQMGPTVLVLSPTRELATQIQAEALKFGKSSKILCTCLYG...

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 IDTkA03G010560
TK1151 IDTkA03G010560
OH-1004 IDLXL04_006125
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)99.800
Protein coverage (%)TK1151 90.339 / OH-1004 82.508
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 IDTkA03G010560
LocationChr03:2666220-2672541 (-)
DescriptionSimilar to RH46: DEAD-box ATP-dependent RNA helicase 46
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g01540 ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.
Characterization of a DEAD box ATPase/RNA helicase protein of Arabidopsis thaliana.1998 · DOI: 10.1093/nar/26.11.2638
At5g14610 DEAD-box ATP-dependent RNA helicase 46. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os01g0549400 ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing. No verified direct reference in this release
Os01g0172200 ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_006125 · 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:0006364 rRNA processing Biological Process
GO:0005634 nucleus Cellular Component
GO:0005730 nucleolus Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003724 RNA helicase activity Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0005524 ATP binding Molecular Function
GO:0016887 ATP hydrolysis activity Molecular Function
KEGG gene cross-reference
ath:AT3G01540
ath:AT5G14610
dosa:Os01g0172200
dosa:Os01g0549400
nsy:104219642
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.

Nucleus0.636
Rank 1 · TkA03G010560 · TK1151
Cytoplasm0.444
Rank 2 · TkA03G010560 · TK1151
Endoplasmic reticulum0.066
Rank 3 · TkA03G010560 · TK1151
Cell membrane0.045
Rank 4 · TkA03G010560 · TK1151
Mitochondrion0.030
Rank 5 · TkA03G010560 · 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.

PF00397WW20-50 aa
PF03700Sorting_nexin53-84 aa
PF03700Sorting_nexin147-159 aa
PF00270DEAD176-345 aa
PF04851ResIII188-339 aa
PF13401AAA_22192-204 aa
PF00271Helicase_C213-274 aa
PF13401AAA_22285-330 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA03G010560PF00397WW20502.7e-0731.2
TkA03G010560PF03700Sorting_nexin53849.87.5
TkA03G010560PF03700Sorting_nexin1471599.87.5
TkA03G010560PF00270DEAD1763453.7e-52177.2
TkA03G010560PF04851ResIII1883392.3e-0938.1
TkA03G010560PF13401AAA_221922040.3511.9
TkA03G010560PF00271Helicase_C2132746.1e-38130.2
TkA03G010560PF13401AAA_222853300.3511.9
TkA03G010560PF16203ERCC3_RAD25_C3724933.7e-0523.9
TkA03G010560PF00271Helicase_C3834916.1e-38130.2
TkA03G010560PF00270DEAD3884543.7e-52177.2
TkA03G010560PF04851ResIII3924362.3e-0938.1
TkA03G010560PF13401AAA_223964490.3511.9
TkA03G010560PF22590Cas3-like_C_23994890.1712.9
TkA03G010560PF00397WW5825852.7e-0731.2

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
Q8H136Arabidopsis thalianasp|Q8H136|RH14_ARATH DEAD-box ATP-dependent RNA helicase 1471.100%Swiss-ProtHigh
Q9LYJ9Arabidopsis thalianasp|Q9LYJ9|RH46_ARATH DEAD-box ATP-dependent RNA helicase 4671.400%Swiss-ProtHigh
Q5JKF2Oryza sativa subsp. japonicasp|Q5JKF2|RH40_ORYSJ DEAD-box ATP-dependent RNA helicase 4072.600%Swiss-ProtHigh
Q5VQL1Oryza sativa subsp. japonicasp|Q5VQL1|RH14_ORYSJ DEAD-box ATP-dependent RNA helicase 1464.200%Swiss-ProtHigh

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