LXL04_026967 | RubberDandelionOmics

Gene overview

LXL04_026967

Reference: OH-1004 Chr: Chr06 Coordinates: 6240581-6243122 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1938 bp · LXL04_026967|LXL04_026967|OH1004|cDNA

ATGGCATCGATTCATGCTACTCTAGCATCAGTTATGTGCAAAAACTCCAACCACTCGACCCTttcaaaaatttcaaaaacatctTTCCTGCCCGTTTTCGACATCACCACCGAAACTACCAACTTATGGAAAAAAGAATCACACATCACAGTTCCTCGAGCCACATTAACCTTCGACCCTCCATCATCAACAAACGTCCCAAAAACCAGTCAACGAAAAAACACAGTCGACCCATCTGCCCCAGATTTCCTTCCACTTCC...

CDS

Download CDS FASTA

1938 bp · LXL04_026967|LXL04_026967|OH1004|CDS

ATGGCATCGATTCATGCTACTCTAGCATCAGTTATGTGCAAAAACTCCAACCACTCGACCCTTTCAAAAATTTCAAAAACATCTTTCCTGCCCGTTTTCGACATCACCACCGAAACTACCAACTTATGGAAAAAAGAATCACACATCACAGTTCCTCGAGCCACATTAACCTTCGACCCTCCATCATCAACAAACGTCCCAAAAACCAGTCAACGAAAAAACACAGTCGACCCATCTGCCCCAGATTTCCTTCCACTTCC...

Protein

Download Protein FASTA

645 aa · LXL04_026967|LXL04_026967|OH1004|PROTEIN

MASIHATLASVMCKNSNHSTLSKISKTSFLPVFDITTETTNLWKKESHITVPRATLTFDPPSSTNVPKTSQRKNTVDPSAPDFLPLPSFEQCFPQSTKEYTEIIHEGSGNILKVPFRRVHLSGDEPHFDTYDTSGPQNISPQIGIPKLRKEWIESREKSNPPRYTQMYFAKQGIVTEEMVYCATRENLDPEFVRSEVARGRAIIPSNKRHLELEPMIVGRNFLVKVNANIGNSAVVSSIEEEVHKLQWATMWGADTIMDL...

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_026967`
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_026967

Location Chr06:6240581-6243122 (-)

Description Similar to THIC: Phosphomethylpyrimidine synthase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g29630`	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.	Vitamin B1 biosynthesis in plants requires the essential iron sulfur cluster protein, THIC.2007 · DOI: 10.1073/pnas.0709597104 AtTHIC, a gene involved in thiamine biosynthesis in Arabidopsis thaliana.2008 · DOI: 10.1038/cr.2008.35

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026967 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009228 thiamine biosynthetic process Biological Process

GO:0009229 thiamine diphosphate biosynthetic process Biological Process

GO:0010266 response to vitamin B1 Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0019904 protein domain specific binding Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0051536 iron-sulfur cluster binding Molecular Function

KEGG gene cross-reference

ath:AT2G29630

bcy:Bcer98_3762

bha:BH1933

pmy:Pmen_0609

psa:PST_3816

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.

Mitochondrion0.591

Rank 1 · LXL04_026967 · OH-1004

Plastid0.206

Rank 2 · LXL04_026967 · OH-1004

Cytoplasm0.171

Rank 3 · LXL04_026967 · OH-1004

Nucleus0.076

Rank 4 · LXL04_026967 · OH-1004

Peroxisome0.041

Rank 5 · LXL04_026967 · 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.

PF13667.12ThiC-associated93-158 aa

PF01964.25ThiC_Rad_SAM165-585 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026967	`PF13667.12`	ThiC-associated	93	158	4.9e-06	27.0
LXL04_026967	`PF01964.25`	ThiC_Rad_SAM	165	585	3.8e-182	606.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O82392`	Arabidopsis thaliana	Phosphomethylpyrimidine synthase, chloroplastic	83.876%	Swiss-Prot	strong database homology

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