LXL04_038942 | RubberDandelionOmics

Gene overview

LXL04_038942

Reference: OH-1004 Chr: Chr09 Coordinates: 53749488-53751342 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

768 bp · LXL04_038942|LXL04_038942|OH1004|cDNA

ATGATTCTTAAACTATGCTTCATTTTGATTACAATTCGCTCTGTATTTGGTGGTTTTGAGGATTTGGTTTGCGAACTTCATCCATCTAATGGGGTTAATTATTCGTATGTTTTAGGGTTTCGAGCAATTGGGAGTGGGATTACGTTATCGGCATTTGCCGCCGTCTTCATCCATATGGGACTTAGTGGCAAAACTCGTCCAGGAAAGAAGTTTCCTAATTTACTTTTCACAATCgaaataaaaaacataaatatgGCCAA...

CDS

Download CDS FASTA

768 bp · LXL04_038942|LXL04_038942|OH1004|CDS

ATGATTCTTAAACTATGCTTCATTTTGATTACAATTCGCTCTGTATTTGGTGGTTTTGAGGATTTGGTTTGCGAACTTCATCCATCTAATGGGGTTAATTATTCGTATGTTTTAGGGTTTCGAGCAATTGGGAGTGGGATTACGTTATCGGCATTTGCCGCCGTCTTCATCCATATGGGACTTAGTGGCAAAACTCGTCCAGGAAAGAAGTTTCCTAATTTACTTTTCACAATCGAAATAAAAAACATAAATATGGCCAA...

Protein

Download Protein FASTA

255 aa · LXL04_038942|LXL04_038942|OH1004|PROTEIN

MILKLCFILITIRSVFGGFEDLVCELHPSNGVNYSYVLGFRAIGSGITLSAFAAVFIHMGLSGKTRPGKKFPNLLFTIEIKNINMAKHGSDSGVYDTHGRFVSSKFEEIFHKYAHTNSDALTSDELDNFIKGNREPKDYGGWNGDYTSIIHGKYSHEETVTTAFFCRKVYYCENMVEATYVCDYILGGQLTIIKAFLEKFKFAMPKGFDPDKDIVKVGVANQTTMLKGETEEIGKLVERTMMQKFGVENIEHSLH

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_038942`
TK1151 ID	TkA04G486670
OH-1004 ID	LXL04_038942
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.300
Protein coverage (%)	TK1151 82.090 / OH-1004 43.137 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_038942

Location Chr09:53749488-53751342 (-)

Description Similar to ISPH: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34350`	Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 1-hydroxy-2-methyl-2-(E)-butenyl 4- diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP).	Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway.2005 · DOI: 10.1105/tpc.104.028860 The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis.2005 · DOI: 10.1104/pp.104.058735
`At1g70670`	Calcium-binding peroxygenase involved in the degradation of storage lipid in oil bodies.	No verified direct reference in this release
`At1g70680`	Calcium-binding peroxygenase involved in the degradation of storage lipid in oil bodies.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0731900`	Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038942 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009737 response to abscisic acid Biological Process

GO:0009819 drought recovery Biological Process

GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Biological Process

GO:0050992 dimethylallyl diphosphate biosynthetic process Biological Process

GO:0005811 lipid droplet Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0004497 monooxygenase activity Molecular Function

GO:0005509 calcium ion binding Molecular Function

GO:0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G70670

ath:AT1G70680

ath:AT4G34350

dosa:Os03g0731900

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.

Extracellular0.255

Rank 1 · LXL04_038942 · OH-1004

Cytoplasm0.235

Rank 2 · LXL04_038942 · OH-1004

Endoplasmic reticulum0.225

Rank 3 · LXL04_038942 · OH-1004

Lysosome / Vacuole0.150

Rank 4 · LXL04_038942 · OH-1004

Mitochondrion0.149

Rank 5 · LXL04_038942 · 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.

PF05042.20Caleosin38-146 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038942	`PF05042.20`	Caleosin	38	146	1.5e-35	123.4

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
`Q94B35`	Arabidopsis thaliana	4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic	65.766%	Swiss-Prot	weak database homology
`Q9CAB7`	Arabidopsis thaliana	Probable peroxygenase 4	56.716%	Swiss-Prot	weak database homology
`Q9CAB8`	Arabidopsis thaliana	Probable peroxygenase 5	64.078%	Swiss-Prot	weak database homology
`Q6AVG6`	Oryza sativa subsp. japonica	4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic	70.270%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card