LXL04_001437 | RubberDandelionOmics

Gene overview

LXL04_001437

Reference: OH-1004 Chr: Chr01 Coordinates: 26770541-26773589 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1641 bp · LXL04_001437|LXL04_001437|OH1004|cDNA

ATGGCTTCCATTAACATGTCTTCCCCATCAACATCTTTACTACGCTCAAAGATGATCACAAACTTCAACTCATACAACAGTCTCCACTCTGTAAATCTCATTTCATCCAATGGCCATACATCAGAGACATTTCTCCACCTCAGCAACAAATCATTCTCCAAAACCAAACCAGATGGTAGACTCAGAGCTTCACTCCTCCCTCTAGATGGTGGTTTCAATCAAAAAAGCATCAATGGTGTTGGTGTATCATCAGGAATTCT...

CDS

Download CDS FASTA

1641 bp · LXL04_001437|LXL04_001437|OH1004|CDS

ATGGCTTCCATTAACATGTCTTCCCCATCAACATCTTTACTACGCTCAAAGATGATCACAAACTTCAACTCATACAACAGTCTCCACTCTGTAAATCTCATTTCATCCAATGGCCATACATCAGAGACATTTCTCCACCTCAGCAACAAATCATTCTCCAAAACCAAACCAGATGGTAGACTCAGAGCTTCACTCCTCCCTCTAGATGGTGGTTTCAATCAAAAAAGCATCAATGGTGTTGGTGTATCATCAGGAATTCT...

Protein

Download Protein FASTA

546 aa · LXL04_001437|LXL04_001437|OH1004|PROTEIN

MASINMSSPSTSLLRSKMITNFNSYNSLHSVNLISSNGHTSETFLHLSNKSFSKTKPDGRLRASLLPLDGGFNQKSINGVGVSSGILIQPDSISLGTLSAETTPTMNSFSNGADEYDLDQPTTGFSSIPEAIEDIRQGKMVVVVDDEDRENEGDLIMAASCVTPEAMAFIVKHGTGIVCVSMKGDDLDRLELPLMVTHKDNEEKLSTAFTVSVDAKHGTTTGVSARDRAATIKALASKDSLPGDFNRPGHIFPLKYREGG...

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_001437`
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_001437

Location Chr01:26770541-26773589 (+)

Description Similar to RIBA1: Bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g64300`	Involved in riboflavin biosynthesis.	Deficiency in riboflavin biosynthesis affects tetrapyrrole biosynthesis in etiolated Arabidopsis tissue.2012 · DOI: 10.1007/s11103-011-9846-1 Arabidopsis RIBA proteins: two out of three isoforms have lost their bifunctional activity in riboflavin biosynthesis.2012 · DOI: 10.3390/ijms131114086
`At2g22450`	Involved in riboflavin biosynthesis.	Arabidopsis RIBA proteins: two out of three isoforms have lost their bifunctional activity in riboflavin biosynthesis.2012 · DOI: 10.3390/ijms131114086
`At5g59750`	Involved in riboflavin biosynthesis.	Arabidopsis RIBA proteins: two out of three isoforms have lost their bifunctional activity in riboflavin biosynthesis.2012 · DOI: 10.3390/ijms131114086

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0481950`	Involved in riboflavin biosynthesis.	No verified direct reference in this release
`Os02g0572400`	Involved in riboflavin biosynthesis.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_001437 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009231 riboflavin biosynthetic process Biological Process

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0003935 GTP cyclohydrolase II activity Molecular Function

GO:0005525 GTP binding Molecular Function

GO:0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G22450

ath:AT5G59750

ath:AT5G64300

dosa:Os02g0572400

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.

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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.

Plastid0.971

Rank 1 · LXL04_001437 · OH-1004

Mitochondrion0.042

Rank 2 · LXL04_001437 · OH-1004

Nucleus0.023

Rank 3 · LXL04_001437 · OH-1004

Cytoplasm0.020

Rank 4 · LXL04_001437 · OH-1004

Cell membrane0.013

Rank 5 · LXL04_001437 · 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.

PF00926.25DHBP_synthase130-322 aa

PF00925.26GTP_cyclohydro2332-498 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001437	`PF00926.25`	DHBP_synthase	130	322	1.5e-85	286.3
LXL04_001437	`PF00925.26`	GTP_cyclohydro2	332	498	6.8e-73	244.4

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
`P47924`	Arabidopsis thaliana	Bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic	77.801%	Swiss-Prot	strong database homology
`Q6NLQ7`	Arabidopsis thaliana	Monofunctional riboflavin biosynthesis protein RIBA 2, chloroplastic	73.684%	Swiss-Prot	strong database homology
`Q9FN89`	Arabidopsis thaliana	Monofunctional riboflavin biosynthesis protein RIBA 3, chloroplastic	64.399%	Swiss-Prot	strong database homology
`Q6Z234`	Oryza sativa subsp. japonica	Probable bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic	79.029%	Swiss-Prot	strong database homology
`Q0E079`	Oryza sativa subsp. japonica	Probable bifunctional riboflavin biosynthesis protein RIBA 2, chloroplastic	66.360%	Swiss-Prot	strong database homology

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