LXL04_009009 | RubberDandelionOmics

Gene overview

LXL04_009009

Reference: OH-1004 Chr: Chr02 Coordinates: 115955985-115958483 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2094 bp · LXL04_009009|LXL04_009009|OH1004|cDNA

ATGGCGGTTCCGACAATAGCACTGTATGCGAGTCCTCCAAGTAGCATTTGCTCAACGCCATATCCATGTCAGATCAATTCACATGGATCCTATGAGTTTGATTTAAACAGCCGTTCGTCGTCTTCGTCGACGGCCACTGCTTCGTCATCGCAAAAATCAATCATTGGCGGACTTTCTTCCCTTTTCTCTTCTTCATCCAGCTTTTCCACCGGCGGAGCGGAAGATTTGACGTTGTTGAGAGGCGGCGAAGAGTTGAGCAA...

CDS

Download CDS FASTA

2094 bp · LXL04_009009|LXL04_009009|OH1004|CDS

ATGGCGGTTCCGACAATAGCACTGTATGCGAGTCCTCCAAGTAGCATTTGCTCAACGCCATATCCATGTCAGATCAATTCACATGGATCCTATGAGTTTGATTTAAACAGCCGTTCGTCGTCTTCGTCGACGGCCACTGCTTCGTCATCGCAAAAATCAATCATTGGCGGACTTTCTTCCCTTTTCTCTTCTTCATCCAGCTTTTCCACCGGCGGAGCGGAAGATTTGACGTTGTTGAGAGGCGGCGAAGAGTTGAGCAA...

Protein

Download Protein FASTA

697 aa · LXL04_009009|LXL04_009009|OH1004|PROTEIN

MAVPTIALYASPPSSICSTPYPCQINSHGSYEFDLNSRSSSSSTATASSSQKSIIGGLSSLFSSSSSFSTGGAEDLTLLRGGEELSNSFSYSPIGSCLKRDHFHHSPVSVIQGPGSLSSTPSMRFSPERDGSFRGGTKRLFKGFVTHALGSCVVYSSSFRMHGNMAEELTFIMDDNNNMKAPNPDPYAKDMLLDAQLKHSIFNDELVIKAFYEAAKAHKGQMRASGDPYLQHCVETAGLLATIGANAMVVAAGLLHDTLD...

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	`LXL04_009009`
TK1151 ID	TkA03G392580
OH-1004 ID	LXL04_009009
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_009009

Location Chr02:115955985-115958483 (+)

Description Similar to RSH3: Probable GTP diphosphokinase RSH3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g54130`	Possesses ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase activity in vitro and is able to functionally complement E.coli relA mutants.	Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana.2008 · DOI: 10.1007/s00425-008-0758-5
`UniProt: Q9M5P5`	Probable ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase that may be involved in a rapid plant ppGpp-mediated response to pathogens and other stresses.	No verified direct reference in this release
`At3g14050`	Possesses ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase activity in vitro and is able to functionally complement E.coli relA mutants.	Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana.2008 · DOI: 10.1007/s00425-008-0758-5
`UniProt: Q9M5P6`	Probable ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase that may be involved in a rapid plant ppGpp-mediated response to pathogens and other stresses.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0457600`	Probable ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase that may be involved in a rapid plant ppGpp-mediated response to pathogens and other stresses.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009009 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009611 response to wounding Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0010150 leaf senescence Biological Process

GO:0015969 guanosine tetraphosphate metabolic process Biological Process

GO:0015970 guanosine tetraphosphate biosynthetic process Biological Process

GO:0015979 photosynthesis Biological Process

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0005524 ATP binding Molecular Function

GO:0005525 GTP binding Molecular Function

GO:0008728 GTP diphosphokinase activity Molecular Function

GO:0016301 kinase activity Molecular Function

KEGG gene cross-reference

ath:AT1G54130

ath:AT3G14050

dosa:Os08g0457600

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.

Plastid0.914

Rank 1 · LXL04_009009 · OH-1004

Mitochondrion0.079

Rank 2 · LXL04_009009 · OH-1004

Nucleus0.055

Rank 3 · LXL04_009009 · OH-1004

Cytoplasm0.047

Rank 4 · LXL04_009009 · OH-1004

Peroxisome0.023

Rank 5 · LXL04_009009 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13328.13HD_4210-364 aa

PF01966.29HD229-333 aa

PF04607.24RelA_SpoT423-533 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009009	`PF13328.13`	HD_4	210	364	2.5e-41	141.7
LXL04_009009	`PF01966.29`	HD	229	333	1.7e-08	35.4
LXL04_009009	`PF04607.24`	RelA_SpoT	423	533	2.5e-41	141.2

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

Protein	Organism	Description	Identity	Database	Confidence
`Q9SYH1`	Arabidopsis thaliana	Probable GTP diphosphokinase RSH3, chloroplastic	64.177%	Swiss-Prot	strong database homology
`Q9M5P5`	Arabidopsis thaliana	Probable GTP diphosphokinase RSH3, chloroplastic	63.900%	Swiss-Prot	strong database homology
`Q9LVJ3`	Arabidopsis thaliana	Probable GTP diphosphokinase RSH2, chloroplastic	63.662%	Swiss-Prot	strong database homology
`Q9M5P6`	Arabidopsis thaliana	Probable GTP diphosphokinase RSH2, chloroplastic	61.983%	Swiss-Prot	strong database homology
`Q7XAP4`	Oryza sativa subsp. japonica	Probable GTP diphosphokinase RSH2, chloroplastic	56.145%	Swiss-Prot	strong database homology

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