TkA03G392940 | RubberDandelionOmics

Gene overview

TkA03G392940

Reference: TK1151 Chr: Chr03 Coordinates: 97462411-97464054 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1611 bp · TkA03G392940|TK1151|cDNA

ATGATCAAGCAAGACACCTTCCTCTTACCCTACTTTCCTCCCAACACAAACCCAAACCAAGAAACGATGTCGTTTGGTGAACCAGACCTAAAGTCAAGCTCTGATCCTTTATCAGATTGGTTAGAAGATTCAATATCGTATCTTCCATCATTCTTAGATGACCCATATGAATCCAACAATCTCATTGATGATGCATGGTGGGCACCCGCTCAAGAACATGAACAACAACTCCTTAACTCTGTTCAAAGTACAAAAACAAC...

CDS

Download CDS FASTA

1611 bp · TkA03G392940|TK1151|CDS

ATGATCAAGCAAGACACCTTCCTCTTACCCTACTTTCCTCCCAACACAAACCCAAACCAAGAAACGATGTCGTTTGGTGAACCAGACCTAAAGTCAAGCTCTGATCCTTTATCAGATTGGTTAGAAGATTCAATATCGTATCTTCCATCATTCTTAGATGACCCATATGAATCCAACAATCTCATTGATGATGCATGGTGGGCACCCGCTCAAGAACATGAACAACAACTCCTTAACTCTGTTCAAAGTACAAAAACAAC...

Protein

Download Protein FASTA

536 aa · TkA03G392940|TK1151|PROTEIN

MIKQDTFLLPYFPPNTNPNQETMSFGEPDLKSSSDPLSDWLEDSISYLPSFLDDPYESNNLIDDAWWAPAQEHEQQLLNSVQSTKTTTTAIVSDQANQLSSDLSKKRKATEELKPVVQVSVKKPVNKRGHGKTTRDGCSNVKSKDGRWAEQLLNPCAAAITAGNVARVRHLLFVLRELASPTGDANYRLAAHGMQALTHHLSSANNRPVKVAVPPVNFSTEKPRFFQLSLINFNDINPWFTIPHNIANNSILQILRDCDH...

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	`TkA03G392940`
TK1151 ID	TkA03G392940
OH-1004 ID	LXL04_002190
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	64.100
Protein coverage (%)	TK1151 99.813 / OH-1004 99.817 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

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Basic Information and Functional Annotation

Gene ID TkA03G392940

Location Chr03:97462411-97464054 (-)

Description Similar to NSP1: Protein NODULATION SIGNALING PATHWAY 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g13840`	Probable transcription factor involved in plant development.	No verified direct reference in this release
`At3g03450`	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway.	Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition.2002 · DOI: 10.1101/gad.969002 Gibberellin regulates Arabidopsis floral development via suppression of DELLA protein function.2004 · DOI: 10.1242/dev.00992 Floral homeotic genes are targets of gibberellin signaling in flower development.2004 · DOI: 10.1073/pnas.0402377101 Loss of function of four DELLA genes leads to light- and gibberellin-independent seed germination in Arabidopsis.2005 · DOI: 10.1007/s00425-005-0057-3 Phytohormone signalling pathways interact with sugars during seed germination and seedling development.2006 · DOI: 10.1093/jxb/erl096 Seed germination of GA-insensitive sleepy1 mutants does not require RGL2 protein disappearance in Arabidopsis.2007 · DOI: 10.1105/tpc.106.048009 Genetic and molecular regulation by DELLA proteins of trichome development in Arabidopsis.2007 · DOI: 10.1104/pp.107.104794 High temperature-induced abscisic acid biosynthesis and its role in the inhibition of gibberellin action in Arabidopsis seeds.2008 · DOI: 10.1104/pp.107.113738 The gibberellic acid signaling repressor RGL2 inhibits Arabidopsis seed germination by stimulating abscisic acid synthesis and ABI5 activity.2008 · DOI: 10.1105/tpc.108.061515 Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis.2010 · DOI: 10.1093/molbev/msq012 A seed coat bedding assay shows that RGL2-dependent release of abscisic acid by the endosperm controls embryo growth in Arabidopsis dormant seeds.2010 · DOI: 10.1073/pnas.1012896107

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0408600`	Transcription factor involved in the control of strigolactone biosynthesis in roots through the activation of the beta-carotene isomerase D27, which participates in a pathway leading to biosynthesis of strigolactones.	Strigolactone biosynthesis in Medicago truncatula and rice requires the symbiotic GRAS-type transcription factors NSP1 and NSP2.2011 · DOI: 10.1105/tpc.111.089771

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002190 · 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:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009610 response to symbiotic fungus Biological Process

GO:0009877 nodulation Biological Process

GO:0042446 hormone biosynthetic process Biological Process

GO:2000032 regulation of secondary shoot formation Biological Process

GO:0005634 nucleus Cellular Component

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0043565 sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G13840

ath:AT3G49950

mtr:11434050

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.887

Rank 1 · TkA03G392940 · TK1151

Cytoplasm0.169

Rank 2 · TkA03G392940 · TK1151

Cell membrane0.037

Rank 3 · TkA03G392940 · TK1151

Endoplasmic reticulum0.029

Rank 4 · TkA03G392940 · TK1151

Plastid0.020

Rank 5 · TkA03G392940 · 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.

PF03514GRAS150-528 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G392940	`PF03514`	GRAS	150	528	1.4e-72	245.4

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
`Q9LRW3`	Arabidopsis thaliana	sp\|Q9LRW3\|SCL29_ARATH Scarecrow-like protein 29	54.800%	Swiss-Prot	High
`Q8GXW1`	Arabidopsis thaliana	sp\|Q8GXW1\|RGL2_ARATH DELLA protein RGL2	24.500%	Swiss-Prot	Low
`Q84MQ9`	Oryza sativa subsp. japonica	sp\|Q84MQ9\|NSP1_ORYSJ Protein NODULATION SIGNALING PATHWAY 1	43.000%	Swiss-Prot	Medium

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