TkA03G558250 | RubberDandelionOmics

Gene overview

TkA03G558250

Reference: TK1151 Chr: Chr03 Coordinates: 141339192-141345100 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2126 bp · TkA03G558250|TK1151|cDNA

CTAAATCTTAAAAAAGTCAAAATCGATTTTGACGTACTACCTCAAACACCGCCAAGACGTCGGCCGTGACGCCGTGTTGTTAGTGAAACTTCCGGTACTGTTAAGCGGAGGGTTTCTTTCCCTAGAGCACCGATCAGGTACAGGGAAATCATCCTTTCTCTACATATCCCCACACCATCAATTCAACATATATGGCGACCTTGCTTCTTCGCAGGAGGCTCTCTCCGTCAACAGTTTCTCGTACTCTTCTCTGCAATGGT...

CDS

Download CDS FASTA

2691 bp · TkA03G558250|TK1151|CDS

ATGAGTTACACACATGGGAATGAAGATAGGCTAAGCCATTTACCTGAAGAGATTCTTTCACGTATACTCTCTTCAATCCCTACAAAATTGGCTGTGCGAACAAGCATCTTATCCAAAAAATGGAGGTACAAATGGACGTTAGTCACAATCCTCGACTTTGACGACGATCGCCCTATCGATGCTTTCCATTCCTTGTCGAATTTTGTAAACCGCGCTTTCAAACTCTGCCAAACATCCAAAATCAAGCGATTCCGGTTACG...

Protein

Download Protein FASTA

896 aa · TkA03G558250|TK1151|PROTEIN

MSYTHGNEDRLSHLPEEILSRILSSIPTKLAVRTSILSKKWRYKWTLVTILDFDDDRPIDAFHSLSNFVNRAFKLCQTSKIKRFRLRLSRYGLQTTSEVKSNISNWIKESVRLNVCEVDLHLTPFEMPVTLFTCKTLTKLSLSGWGMEGYVGSNVSIILPLLKTLHITSPINFPGRVSVNSFRLIHSCPMLESLSLEIAMCNNQEDYNFNIATLKRLKLKIVSVLSLNKVILNLPNLESLSFAGLLRSLFVVKDLSSLVD...

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	`TkA03G558250`
TK1151 ID	TkA03G558250
OH-1004 ID	LXL04_010956
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	89.300
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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 ID TkA03G558250

Location Chr03:141339192-141345100 (-)

Description Similar to SUV3: DExH-box ATP-dependent RNA helicase DExH16, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g14790`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release
`At5g39840`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0746500`	Major helicase player in mitochondrial RNA metabolism.	OsSUV3 dual helicase functions in salinity stress tolerance by maintaining photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. IR64).2013 · DOI: 10.1111/tpj.12277 OsSUV3 transgenic rice maintains higher endogenous levels of plant hormones that mitigates adverse effects of salinity and sustains crop productivity.2014 · DOI: 10.1186/s12284-014-0017-2
`UniProt: Q01IJ3`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release
`Os04g0459800`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010956 · 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:0000965 mitochondrial RNA 3'-end processing Biological Process

GO:0009555 pollen development Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009736 cytokinin-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009939 positive regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0010929 positive regulation of auxin mediated signaling pathway Biological Process

GO:0016070 RNA metabolic process Biological Process

GO:0080038 positive regulation of cytokinin-activated signaling pathway Biological Process

GO:1901002 positive regulation of response to salt stress Biological Process

KEGG gene cross-reference

ath:AT4G14790

ath:AT5G39840

dosa:Os03g0746500

dosa:Os04g0459800

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.

Nucleus0.513

Rank 1 · TkA03G558250 · TK1151

Plastid0.243

Rank 2 · TkA03G558250 · TK1151

Cytoplasm0.170

Rank 3 · TkA03G558250 · TK1151

Mitochondrion0.090

Rank 4 · TkA03G558250 · TK1151

Cell membrane0.026

Rank 5 · TkA03G558250 · 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.

PF00646F-box11-46 aa

PF12937F-box-like11-42 aa

PF00646F-box121-137 aa

PF22527DEXQc_Suv3407-560 aa

PF00271Helicase_C580-686 aa

PF18147Suv3_C_1768-809 aa

PF12513SUV3_C834-881 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G558250	`PF00646`	F-box	11	46	7.7e-06	26.3
TkA03G558250	`PF12937`	F-box-like	11	42	0.0051	17.3
TkA03G558250	`PF00646`	F-box	121	137	7.7e-06	26.3
TkA03G558250	`PF22527`	DEXQc_Suv3	407	560	1.4e-65	220.3
TkA03G558250	`PF00271`	Helicase_C	580	686	2.2e-12	47.9
TkA03G558250	`PF18147`	Suv3_C_1	768	809	5.2e-09	36.6
TkA03G558250	`PF12513`	SUV3_C	834	881	7.1e-16	58.5

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

Protein	Organism	Description	Identity	Database	Confidence
`Q9SMX1`	Arabidopsis thaliana	sp\|Q9SMX1\|SUV3M_ARATH DExH-box ATP-dependent RNA helicase DExH16, mitochondrial	72.100%	Swiss-Prot	Medium
`F4KFV7`	Arabidopsis thaliana	sp\|F4KFV7\|SUV3L_ARATH DExH-box ATP-dependent RNA helicase DExH18, mitochondrial	40.400%	Swiss-Prot	Medium
`Q10D00`	Oryza sativa subsp. japonica	sp\|Q10D00\|SUV3M_ORYSJ ATP-dependent RNA helicase SUV3, mitochondrial	71.600%	Swiss-Prot	Medium
`Q01IJ3`	Oryza sativa subsp. indica	sp\|Q01IJ3\|SUV3L_ORYSI ATP-dependent RNA helicase SUV3L, mitochondrial	42.000%	Swiss-Prot	Medium
`Q7X745`	Oryza sativa subsp. japonica	sp\|Q7X745\|SUV3L_ORYSJ ATP-dependent RNA helicase SUV3L, mitochondrial	42.000%	Swiss-Prot	Medium

JBrowse

View in Genome Browser

Gene Card