LXL04_029590 | RubberDandelionOmics

Gene overview

LXL04_029590

Reference: OH-1004 Chr: Chr06 Coordinates: 94924760-94926028 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

696 bp · LXL04_029590|LXL04_029590|OH1004|cDNA

ATGGCGACTACCTCATCGTGTTACACATCTCCGCTACACACCGGAGTCTACTCGAAACAACAATCAGTTCTTCCTTCTTCCGCCTCCCTCCTCACCTGCGCCACCAGACGCTCACCCATCTCTCTTCGGTCGATACCACGGCCGGTGGTAGTTGCGGCAGCCGCCAACGCCGTTGAAGTTGAGAAACAGGCCGTCGCGCCAACGCCTTCGAAAGTTCTCCCGTTCCGAGTCGGCCACGGATTCGATCTTCATAGATTGGA...

CDS

Download CDS FASTA

696 bp · LXL04_029590|LXL04_029590|OH1004|CDS

ATGGCGACTACCTCATCGTGTTACACATCTCCGCTACACACCGGAGTCTACTCGAAACAACAATCAGTTCTTCCTTCTTCCGCCTCCCTCCTCACCTGCGCCACCAGACGCTCACCCATCTCTCTTCGGTCGATACCACGGCCGGTGGTAGTTGCGGCAGCCGCCAACGCCGTTGAAGTTGAGAAACAGGCCGTCGCGCCAACGCCTTCGAAAGTTCTCCCGTTCCGAGTCGGCCACGGATTCGATCTTCATAGATTGGA...

Protein

Download Protein FASTA

231 aa · LXL04_029590|LXL04_029590|OH1004|PROTEIN

MATTSSCYTSPLHTGVYSKQQSVLPSSASLLTCATRRSPISLRSIPRPVVVAAAANAVEVEKQAVAPTPSKVLPFRVGHGFDLHRLEPGYPLIIGGINIPHDRGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAASSVFIKEAVRLMDEAGYELGNLDATLILQRPKVSPHKEAIRANLSLLLGADPSVVNLKAKTHEKVDSLGENRSIAAHTVVLLMKK

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_029590`
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_029590

Location Chr06:94924760-94926028 (+)

Description Similar to ISPF: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g63970`	Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2- phosphate into 2C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP.	Functional evidence for the involvement of Arabidopsis IspF homolog in the nonmevalonate pathway of plastid isoprenoid biosynthesis.2006 · DOI: 10.1007/s00425-005-0140-9

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0680600`	Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate into 2C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP (Probable).	A single nucleotide mutation of IspF gene involved in the MEP pathway for isoprenoid biosynthesis causes yellow-green leaf phenotype in rice.2018 · DOI: 10.1007/s11103-017-0668-7

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029590 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0015995 chlorophyll biosynthetic process Biological Process

GO:0016114 terpenoid biosynthetic process Biological Process

GO:0016117 carotenoid biosynthetic process Biological Process

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

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G63970

bav:BAV1059

dosa:Os02g0680600

gwc:GWCH70_0087

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.

Plastid0.987

Rank 1 · LXL04_029590 · OH-1004

Mitochondrion0.027

Rank 2 · LXL04_029590 · OH-1004

Cytoplasm0.026

Rank 3 · LXL04_029590 · OH-1004

Peroxisome0.020

Rank 4 · LXL04_029590 · OH-1004

Nucleus0.016

Rank 5 · LXL04_029590 · 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.

PF02542.22YgbB75-228 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029590	`PF02542.22`	YgbB	75	228	2.5e-60	204.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9CAK8`	Arabidopsis thaliana	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic	89.017%	Swiss-Prot	strong database homology
`Q6EPN6`	Oryza sativa subsp. japonica	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic	70.259%	Swiss-Prot	strong database homology

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