LXL04_021396 | RubberDandelionOmics

Gene overview

LXL04_021396

Reference: OH-1004 Chr: Chr04 Coordinates: 128722867-128723512 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

516 bp · LXL04_021396|LXL04_021396|OH1004|cDNA

ATGAACAGATCCCTTCATCCCAAACAACAACCATCATTTCTTCATCCCTTCATCACATCCATTTTTCGAATCACAAAAGCGATGTTCGATTTAGTATCTATGAAGAGATCAATTTCATTTTCGGAAGATCAGGTCAACGGAGAGGGTGATGTTGATGGTGGCAAGATGAAAAAGAAGATCGGGGAAGATCTGGTACCAGATACAGAGATTTTAGGTGAGGAGGACCCGGAGAACTCGGATATGGCGGGCAACCTCATCAT...

CDS

Download CDS FASTA

516 bp · LXL04_021396|LXL04_021396|OH1004|CDS

ATGAACAGATCCCTTCATCCCAAACAACAACCATCATTTCTTCATCCCTTCATCACATCCATTTTTCGAATCACAAAAGCGATGTTCGATTTAGTATCTATGAAGAGATCAATTTCATTTTCGGAAGATCAGGTCAACGGAGAGGGTGATGTTGATGGTGGCAAGATGAAAAAGAAGATCGGGGAAGATCTGGTACCAGATACAGAGATTTTAGGTGAGGAGGACCCGGAGAACTCGGATATGGCGGGCAACCTCATCAT...

Protein

Download Protein FASTA

171 aa · LXL04_021396|LXL04_021396|OH1004|PROTEIN

MNRSLHPKQQPSFLHPFITSIFRITKAMFDLVSMKRSISFSEDQVNGEGDVDGGKMKKKIGEDLVPDTEILGEEDPENSDMAGNLIIISTVTLTIRIRSRTTHTKWNLWGLQETEQVNDEKLFVLKLEETGRGVLVYLRGHEGRGIGLGHKLRAYNLIRQIGNHEAFRLEF

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_021396`
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_021396

Location Chr04:128722867-128723512 (-)

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
`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
`Os05g0460600`	Involved in riboflavin biosynthesis.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021396 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009231 riboflavin biosynthetic process Biological Process

GO:0005829 cytosol 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:AT5G59750

ath:AT5G64300

dosa:Os02g0572400

dosa:Os05g0460600

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.

Nucleus0.375

Rank 1 · LXL04_021396 · OH-1004

Cytoplasm0.336

Rank 2 · LXL04_021396 · OH-1004

Mitochondrion0.171

Rank 3 · LXL04_021396 · OH-1004

Cell membrane0.107

Rank 4 · LXL04_021396 · OH-1004

Endoplasmic reticulum0.075

Rank 5 · LXL04_021396 · 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.

PF00925.26GTP_cyclohydro2124-160 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021396	`PF00925.26`	GTP_cyclohydro2	124	160	6.1e-08	33.1

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	53.968%	Swiss-Prot	weak database homology
`Q9FN89`	Arabidopsis thaliana	Monofunctional riboflavin biosynthesis protein RIBA 3, chloroplastic	50.794%	Swiss-Prot	weak database homology
`Q6Z234`	Oryza sativa subsp. japonica	Probable bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic	52.381%	Swiss-Prot	weak database homology
`Q0E079`	Oryza sativa subsp. japonica	Probable bifunctional riboflavin biosynthesis protein RIBA 2, chloroplastic	90.323%	Swiss-Prot	weak database homology
`Q6L506`	Oryza sativa subsp. japonica	Probable monofunctional riboflavin biosynthesis protein RIBA 3, chloroplastic	83.871%	Swiss-Prot	weak database homology

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