TkA03G466320 | RubberDandelionOmics

Gene overview

TkA03G466320

Reference: TK1151 Chr: Chr03 Coordinates: 116418589-116421603 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2213 bp · TkA03G466320|TK1151|cDNA

ATACCCAGCCACCGCCCTTGGCAATAGGCCAATGACTTGCCCCCTTTTCCCTTCTCTCATTTCGTAAACCCTCACCCCCTCAAAAATTAGGGTTTTACAATCCGTCTTCATCACACACAGTACCCACACACAGAAGCGACAGACGATCACAAATTGATTTGCAAAATGAATAGTCTACTCTTCAGAACATCTTCCAGGCGACTCACTAACCTTGCTTCCCTTACTACCTGCAACCCACTGAAACACCTTGCTCCATCATC...

CDS

Download CDS FASTA

1578 bp · TkA03G466320|TK1151|CDS

ATGAATAGTCTACTCTTCAGAACATCTTCCAGGCGACTCACTAACCTTGCTTCCCTTACTACCTGCAACCCACTGAAACACCTTGCTCCATCATCCACACCACCCTCACCTGCAAATCATACGGAATTACCCATCCAATCTCAATCTTCCCATTCAAATGTTGGGTTTTTGAGGAGTTTTCACGGGTCTCGATGGGTGAGTATCAAAGCTTCCGATGTGTCGACACAAGCTGCGGGATACGCGGTTGCCGCCGATCACTC...

Protein

Download Protein FASTA

525 aa · TkA03G466320|TK1151|PROTEIN

MNSLLFRTSSRRLTNLASLTTCNPLKHLAPSSTPPSPANHTELPIQSQSSHSNVGFLRSFHGSRWVSIKASDVSTQAAGYAVAADHSYDGDRAASSDGLEISKLGINQEIVTALEKKGITKLFPIQRAVLEPAMQGRDMIGRARTGTGKTLAFGIPIMDKIIKYNEKHGRGRNPLAIVLAPTRELARQVEKEFYESAPNLDTLCVYGGSPIQRQMSTLDRGVDIIVGTPGRVIDLLKRGALNLSEVKFAVLDEADQMLNV...

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	`TkA03G466320`
TK1151 ID	TkA03G466320
OH-1004 ID	LXL04_039027
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	53.600
Protein coverage (%)	TK1151 86.286 / OH-1004 62.225 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 TkA03G466320

Location Chr03:116418589-116421603 (-)

Description Similar to RH3A: DEAD-box ATP-dependent RNA helicase 3A, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g22330`	DEAD-box ATP-dependent RNA helicase 53, mitochondrial.	No verified direct reference in this release
`At3g22310`	DEAD-box ATP-dependent RNA helicase 9, mitochondrial.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0143700`	DEAD-box ATP-dependent RNA helicase 53.	No verified direct reference in this release
`Os12g0611200`	DEAD-box ATP-dependent RNA helicase 9.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_039027 · 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:0000373 Group II intron splicing Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0042254 ribosome biogenesis Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0051607 defense response to virus Biological Process

GO:2000637 positive regulation of miRNA-mediated gene silencing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

KEGG gene cross-reference

ath:AT5G26742

dosa:Os03g0827700

dosa:Os07g0143700

zma:100191761

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.

Mitochondrion0.626

Rank 1 · TkA03G466320 · TK1151

Plastid0.364

Rank 2 · TkA03G466320 · TK1151

Nucleus0.044

Rank 3 · TkA03G466320 · TK1151

Cytoplasm0.030

Rank 4 · TkA03G466320 · TK1151

Cell membrane0.008

Rank 5 · TkA03G466320 · 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.

PF00270DEAD124-290 aa

PF13604AAA_30125-254 aa

PF04851ResIII140-286 aa

PF00271Helicase_C170-220 aa

PF14617CMS1222-254 aa

PF13604AAA_30294-313 aa

PF00271Helicase_C337-438 aa

PF13604AAA_30341-365 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G466320	`PF00270`	DEAD	124	290	1.9e-46	158.5
TkA03G466320	`PF13604`	AAA_30	125	254	0.028	14.9
TkA03G466320	`PF04851`	ResIII	140	286	8e-05	23.3
TkA03G466320	`PF00271`	Helicase_C	170	220	1.8e-33	115.8
TkA03G466320	`PF14617`	CMS1	222	254	0.0024	18.0
TkA03G466320	`PF13604`	AAA_30	294	313	0.028	14.9
TkA03G466320	`PF00271`	Helicase_C	337	438	1.8e-33	115.8
TkA03G466320	`PF13604`	AAA_30	341	365	0.028	14.9
TkA03G466320	`PF00270`	DEAD	342	400	1.9e-46	158.5
TkA03G466320	`PF16203`	ERCC3_RAD25_C	342	420	0.0074	16.3
TkA03G466320	`PF22590`	Cas3-like_C_2	344	437	0.27	12.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LUW5`	Arabidopsis thaliana	sp\|Q9LUW5\|RH53_ARATH DEAD-box ATP-dependent RNA helicase 53, mitochondrial	77.000%	Swiss-Prot	High
`Q9LUW6`	Arabidopsis thaliana	sp\|Q9LUW6\|RH9_ARATH DEAD-box ATP-dependent RNA helicase 9, mitochondrial	73.300%	Swiss-Prot	High
`Q0D8N0`	Oryza sativa subsp. japonica	sp\|Q0D8N0\|RH53_ORYSJ DEAD-box ATP-dependent RNA helicase 53	69.200%	Swiss-Prot	High
`Q0ILZ4`	Oryza sativa subsp. japonica	sp\|Q0ILZ4\|RH9_ORYSJ DEAD-box ATP-dependent RNA helicase 9	70.400%	Swiss-Prot	High

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