LXL04_006972 | RubberDandelionOmics

Gene overview

LXL04_006972

Reference: OH-1004 Chr: Chr02 Coordinates: 32633154-32634586 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

876 bp · LXL04_006972|LXL04_006972|OH1004|cDNA

ATGATTGTAACAGTGAACCATGGAGTGTCATACAATAAGCACATCAACACAAGGATTGTTATCAGGGTAAGACTTTTATACATCCGGATTCAATGCAGTAACAAACACATATCATGGATTTTATGGCCAAATAGAAGCTCAAGTCTTTCAAATTCACATAAACTTCAGTATCTGAAAAATAGTATTCGCCACCCCCATTGGAGAACACTTTGTATACCTACCACTCTTCATGAAGAATATTCATCAATCCAGTCCAAAAA...

CDS

Download CDS FASTA

876 bp · LXL04_006972|LXL04_006972|OH1004|CDS

ATGATTGTAACAGTGAACCATGGAGTGTCATACAATAAGCACATCAACACAAGGATTGTTATCAGGGTAAGACTTTTATACATCCGGATTCAATGCAGTAACAAACACATATCATGGATTTTATGGCCAAATAGAAGCTCAAGTCTTTCAAATTCACATAAACTTCAGTATCTGAAAAATAGTATTCGCCACCCCCATTGGAGAACACTTTGTATACCTACCACTCTTCATGAAGAATATTCATCAATCCAGTCCAAAAA...

Protein

Download Protein FASTA

291 aa · LXL04_006972|LXL04_006972|OH1004|PROTEIN

MIVTVNHGVSYNKHINTRIVIRVRLLYIRIQCSNKHISWILWPNRSSSLSNSHKLQYLKNSIRHPHWRTLCIPTTLHEEYSSIQSKKNSNSDEFDQPIDNDQLMALLADAERAKLLRKLSEANQHNRYLKRQLLVREDSIAQFKSELAITELEIQGLLNMAKEIVGYGIPGGSRKINGKYIQSLLLLQLQGVQEKLKKQIKEVELAQSKEVWLYWSGMAESVQVMGSFDGWSHGDDLSAEYTGSYTRFSTSIMLRPGRYE...

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_006972`
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_006972

Location Chr02:32633154-32634586 (-)

Description Similar to PTST: Protein PTST, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g39790`	Involved in targeting GBSS1 to the starch granule.	Arabidopsis At5g39790 encodes a chloroplast-localized, carbohydrate-binding, coiled-coil domain-containing putative scaffold protein.2008 · DOI: 10.1186/1471-2229-8-120
`At5g03420`	Involved in starch granule initiation in leaf chloroplasts.	No verified direct reference in this release
`At1g27070`	Involved in starch granule initiation in leaf chloroplasts.	Homologs of PROTEIN TARGETING TO STARCH Control Starch Granule Initiation in Arabidopsis Leaves.2017 · DOI: 10.1105/tpc.17.00222 Two Plastidial Coiled-Coil Proteins Are Essential for Normal Starch Granule Initiation in Arabidopsis.2018 · DOI: 10.1105/tpc.18.00219

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0686900`	Involved in compound starch granule formation and starch synthesis in endosperm.	FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice endosperm.2014 · DOI: 10.1111/tpj.12444

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006972 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006633 fatty acid biosynthetic process Biological Process

GO:0010581 regulation of starch biosynthetic process Biological Process

GO:0019252 starch biosynthetic process Biological Process

GO:2000014 regulation of endosperm development Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009569 chloroplast starch grain Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0030247 polysaccharide binding Molecular Function

GO:2001066 amylopectin binding Molecular Function

KEGG gene cross-reference

ath:AT1G27070

ath:AT5G03420

ath:AT5G39790

dosa:Os03g0686900

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.

Plastid0.966

Rank 1 · LXL04_006972 · OH-1004

Nucleus0.037

Rank 2 · LXL04_006972 · OH-1004

Mitochondrion0.033

Rank 3 · LXL04_006972 · OH-1004

Cytoplasm0.026

Rank 4 · LXL04_006972 · OH-1004

Peroxisome0.017

Rank 5 · LXL04_006972 · 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.

PF16561.12AMPK1_CBM212-280 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006972	`PF16561.12`	AMPK1_CBM	212	280	7.7e-15	55.6

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
`Q94AX2`	Arabidopsis thaliana	Protein PTST, chloroplastic	63.500%	Swiss-Prot	moderate database homology
`F4KFB3`	Arabidopsis thaliana	Protein PTST homolog 3, chloroplastic	39.837%	Swiss-Prot	weak database homology
`Q9LFY0`	Arabidopsis thaliana	Protein PTST homolog 2, chloroplastic	46.154%	Swiss-Prot	weak database homology
`Q10F03`	Oryza sativa subsp. japonica	Protein FLOURY ENDOSPERM 6, chloroplastic	37.273%	Swiss-Prot	weak database homology

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