TkA03G442960 | RubberDandelionOmics

Gene overview

TkA03G442960

Reference: TK1151 Chr: Chr03 Coordinates: 110388227-110392087 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2291 bp · TkA03G442960|TK1151|cDNA

GGAAAATATCATTCGTTCCCTGCCCCTCTTTTCCTTCCATCAGATCAGTCAAACTCTCGAGCGCTTTTCAAAACCCTAACCTGGAATTGGGAAATATCGTTGATTTCGACCTCCAATTTTACTCAACCGTGATGAATCATTACGACTCCAGAATTGCGGACACTGGTTCTTACCATCAACGTCGGAGTGATTTTATGGGATTACCGCATTCGTCGGGACCCCCTGCCGGTGCTGCTTCAAACTATGTCCGCGGCGGACCG...

CDS

Download CDS FASTA

1539 bp · TkA03G442960|TK1151|CDS

ATGGAAGAGGAGGGAGAGGTTTCAGTTCTGGGAGAGGGGTGGTGGAAGAACAAGCATGGAGGCTTTGATAGCGGTAGAAGCAGAGGAGGAAGAGGTGGTGGCTCTAAAGGAGACTTGGATAGTATAGCTTTACCAAAACAAGATTTTATCAACTTGGTACCATTCGAGAAGAACTTCTATCGCGAGTCTCCATCTGTAAGTGACATGACTGATCAAGAGGTGGCAGTTTACCGTGGCAGGAGGGAGATCACTGTTGAAGG...

Protein

Download Protein FASTA

512 aa · TkA03G442960|TK1151|PROTEIN

MEEEGEVSVLGEGWWKNKHGGFDSGRSRGGRGGGSKGDLDSIALPKQDFINLVPFEKNFYRESPSVSDMTDQEVAVYRGRREITVEGHDVPKPIRMFHEAGFPGYCLDVIARLGFIEPTPIQAQGWPMALKGRDLIGIAETGSGKTLSYLLPAVVHVSAQPPLVYGDGPIVLVLAPTRELAVQIQQEAGKFSSQSNIRSTCIYGGAPKGPQIRDLQRGVEIVIGTPGRLIDMLEARHTNLKRVTYLVLDEADRMLDMGFE...

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.

ID Mapping

Input ID	`TkA03G442960`
TK1151 ID	TkA03G442960
OH-1004 ID	LXL04_009501
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.800
Protein coverage (%)	TK1151 93.359 / OH-1004 74.804 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 version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G442960

Location Chr03:110388227-110392087 (+)

Description Similar to RH30: DEAD-box ATP-dependent RNA helicase 30

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g63120`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release
`At1g55150`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0911100`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release
`Os01g0197200`	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_009501 · 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:0000380 alternative mRNA splicing, via spliceosome Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0002151 G-quadruplex RNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ani:ANIA_05931

ath:AT1G55150

ath:AT5G63120

kla:KLLA0_F23716g

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.

Nucleus0.630

Rank 1 · TkA03G442960 · TK1151

Cytoplasm0.488

Rank 2 · TkA03G442960 · TK1151

Endoplasmic reticulum0.054

Rank 3 · TkA03G442960 · TK1151

Cell membrane0.048

Rank 4 · TkA03G442960 · TK1151

Mitochondrion0.033

Rank 5 · TkA03G442960 · 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.

PF00270DEAD119-289 aa

PF04851ResIII139-283 aa

PF00271Helicase_C171-211 aa

PF14617CMS1219-250 aa

PF00271Helicase_C280-303 aa

PF00271Helicase_C326-435 aa

PF04851ResIII329-360 aa

PF00270DEAD333-413 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G442960	`PF00270`	DEAD	119	289	9e-51	172.6
TkA03G442960	`PF04851`	ResIII	139	283	1.5e-05	25.7
TkA03G442960	`PF00271`	Helicase_C	171	211	5.8e-33	114.2
TkA03G442960	`PF14617`	CMS1	219	250	0.17	11.9
TkA03G442960	`PF00271`	Helicase_C	280	303	5.8e-33	114.2
TkA03G442960	`PF00271`	Helicase_C	326	435	5.8e-33	114.2
TkA03G442960	`PF04851`	ResIII	329	360	1.5e-05	25.7
TkA03G442960	`PF00270`	DEAD	333	413	9e-51	172.6
TkA03G442960	`PF13344`	Hydrolase_6	436	468	0.15	12.9

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

Protein	Organism	Description	Identity	Database	Confidence
`Q8W4R3`	Arabidopsis thaliana	sp\|Q8W4R3\|RH30_ARATH DEAD-box ATP-dependent RNA helicase 30	73.300%	Swiss-Prot	High
`Q9C718`	Arabidopsis thaliana	sp\|Q9C718\|RH20_ARATH DEAD-box ATP-dependent RNA helicase 20	73.300%	Swiss-Prot	High
`Q5N7W4`	Oryza sativa subsp. japonica	sp\|Q5N7W4\|RH30_ORYSJ DEAD-box ATP-dependent RNA helicase 30	72.000%	Swiss-Prot	High
`Q5QMN3`	Oryza sativa subsp. japonica	sp\|Q5QMN3\|RH20_ORYSJ DEAD-box ATP-dependent RNA helicase 20	72.100%	Swiss-Prot	High

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