LXL04_036041 | RubberDandelionOmics

Gene overview

LXL04_036041

Reference: OH-1004 Chr: Chr08 Coordinates: 34575956-34582965 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3141 bp · LXL04_036041|LXL04_036041|OH1004|cDNA

ATGAAACATCCCAACAGTCATCAAAACGCAAAGTACAGAGTTCTCTACTTCTATGCACTTACcttcaacatcatcatcaagaaaataaaaaagatgATGCAGTCTGAGCTTTTAGTTCAGACCTCTTGGCCACCTCAATCTCATTTTCATTCAAAACTTGATCCTTATAATCCAAACATGGGTTTTTATGAGATTGAACACCAAGAAATTCATTCCTCAATTAACAGCACCCCAGAAAACTCATTATTCGGTTATGAATC...

CDS

Download CDS FASTA

3141 bp · LXL04_036041|LXL04_036041|OH1004|CDS

ATGAAACATCCCAACAGTCATCAAAACGCAAAGTACAGAGTTCTCTACTTCTATGCACTTACCTTCAACATCATCATCAAGAAAATAAAAAAGATGATGCAGTCTGAGCTTTTAGTTCAGACCTCTTGGCCACCTCAATCTCATTTTCATTCAAAACTTGATCCTTATAATCCAAACATGGGTTTTTATGAGATTGAACACCAAGAAATTCATTCCTCAATTAACAGCACCCCAGAAAACTCATTATTCGGTTATGAATC...

Protein

Download Protein FASTA

1046 aa · LXL04_036041|LXL04_036041|OH1004|PROTEIN

MKHPNSHQNAKYRVLYFYALTFNIIIKKIKKMMQSELLVQTSWPPQSHFHSKLDPYNPNMGFYEIEHQEIHSSINSTPENSLFGYESYDQIQNLSTIDNDSHNISTLDDVCRWLCDENQGIEEMESDRSTESVHACSPDLSMTSSDDVMELESQSGVEDLLKAYADAMEMGQKELANVIVTCIGEKINPIGPAIDRIAFNLFKSAENQGDEYLKEELMRNFKPAFRAFYDIFPYGRFVHFTANSAILEAVPSDVESIHIV...

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_036041`
TK1151 ID	TkA04G082290
OH-1004 ID	LXL04_036041
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	79.800
Protein coverage (%)	TK1151 99.465 / OH-1004 34.608 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_036041

Location Chr08:34575956-34582965 (+)

Description Similar to NSP2: Protein NODULATION SIGNALING PATHWAY 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g08250`	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
`At5g17490`	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_036041 · GCA_047496595.1_OSU_TarKok_2.0.

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:0005634 nucleus Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0031965 nuclear membrane Cellular Component

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0043565 sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

ath:AT4G08250

mtr:11406790

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.

Cytoplasm0.603

Rank 1 · LXL04_036041 · OH-1004

Nucleus0.457

Rank 2 · LXL04_036041 · OH-1004

Cell membrane0.081

Rank 3 · LXL04_036041 · OH-1004

Endoplasmic reticulum0.054

Rank 4 · LXL04_036041 · OH-1004

Plastid0.030

Rank 5 · LXL04_036041 · OH-1004

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.

PF03514.21GRAS158-510 aa

PF03514.21GRAS696-1045 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036041	`PF03514.21`	GRAS	158	510	1.2e-86	291.7
LXL04_036041	`PF03514.21`	GRAS	696	1045	1.2e-86	291.7

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
`Q9SUF5`	Arabidopsis thaliana	Scarecrow-like protein 26	26.515%	Swiss-Prot	weak database homology
`Q8GXW1`	Arabidopsis thaliana	DELLA protein RGL2	23.937%	Swiss-Prot	weak database homology
`Q9LF53`	Arabidopsis thaliana	DELLA protein RGL3	22.685%	Swiss-Prot	weak database homology

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