LXL04_013419 | RubberDandelionOmics

Gene overview

LXL04_013419

Reference: OH-1004 Chr: Chr03 Coordinates: 29329511-29332378 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1809 bp · LXL04_013419|LXL04_013419|OH1004|cDNA

ATGGCTACAATATCAGTAGCAGATGTCGCCTTCCAGACCCATCCACACCACTTTTTTGTTTCCTCAAGCATTAGTGGATCTAAACTGTATGTCAATCCCAAGAAATATCCTCTCAACTGTAGAAAACACTCCAATAGTAAAAGAAAATTCTTACACAAAAGTGACTCTGTATTCAAATCAAGGAACTTCATGTGCTGTAGTGTGGAAACAAAAATATCACAAGATACAACAGCTGTTGACAATGGTGGAAGATTAGCACT...

CDS

Download CDS FASTA

1809 bp · LXL04_013419|LXL04_013419|OH1004|CDS

ATGGCTACAATATCAGTAGCAGATGTCGCCTTCCAGACCCATCCACACCACTTTTTTGTTTCCTCAAGCATTAGTGGATCTAAACTGTATGTCAATCCCAAGAAATATCCTCTCAACTGTAGAAAACACTCCAATAGTAAAAGAAAATTCTTACACAAAAGTGACTCTGTATTCAAATCAAGGAACTTCATGTGCTGTAGTGTGGAAACAAAAATATCACAAGATACAACAGCTGTTGACAATGGTGGAAGATTAGCACT...

Protein

Download Protein FASTA

602 aa · LXL04_013419|LXL04_013419|OH1004|PROTEIN

MATISVADVAFQTHPHHFFVSSSISGSKLYVNPKKYPLNCRKHSNSKRKFLHKSDSVFKSRNFMCCSVETKISQDTTAVDNGGRLALVVDDDSYKSKLLTDGPRREIPEWMARRIGSVRPKFPPKKIDISEANTSKFKSLQLPNPSEVWSIAKAKPKDGDSLMGNVMEKELIEKKRKALERALQRKTVQWQKTPEEIKLEPGTGTGREIVFQGFNWESCRKKWYLDLAPKAADLSRCGITAVWLPPPTQSVAPQGYMPSD...

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_013419`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013419

Location Chr03:29329511-29332378 (-)

Description Similar to AMY3: Alpha-amylase 3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g69830`	Possesses endoamylolytic activity in vitro, but seems not required for breakdown of transitory starch in leaves.	alpha-Amylase is not required for breakdown of transitory starch in Arabidopsis leaves.2005 · DOI: 10.1074/jbc.m413638200 Starch granule biosynthesis in Arabidopsis is abolished by removal of all debranching enzymes but restored by the subsequent removal of an endoamylase.2008 · DOI: 10.1105/tpc.108.063487 Arabidopsis thaliana AMY3 is a unique redox-regulated chloroplastic α-amylase.2013 · DOI: 10.1074/jbc.m113.514794 Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants.2016 · DOI: 10.1105/tpc.16.00143
`At1g76130`	Probable alpha-amylase that does not seem to be required for breakdown of transitory starch in leaves.	alpha-Amylase is not required for breakdown of transitory starch in Arabidopsis leaves.2005 · DOI: 10.1074/jbc.m413638200

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2YGY2`	Important for breakdown of endosperm starch during germination.	No verified direct reference in this release
`Os06g0713800`	Important for breakdown of endosperm starch during germination.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013419 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005983 starch catabolic process Biological Process

GO:0005987 sucrose catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0004556 alpha-amylase activity Molecular Function

GO:0005509 calcium ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G69830

ath:AT1G76130

dosa:Os06g0713800

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.

Plastid0.963

Rank 1 · LXL04_013419 · OH-1004

Mitochondrion0.040

Rank 2 · LXL04_013419 · OH-1004

Cytoplasm0.034

Rank 3 · LXL04_013419 · OH-1004

Cell membrane0.027

Rank 4 · LXL04_013419 · OH-1004

Nucleus0.024

Rank 5 · LXL04_013419 · 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.

PF00128.32Alpha-amylase235-299 aa

PF07821.19Alpha-amyl_C2538-599 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013419	`PF00128.32`	Alpha-amylase	235	299	5.5e-13	49.6
LXL04_013419	`PF07821.19`	Alpha-amyl_C2	538	599	1.6e-15	57.9

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
`Q94A41`	Arabidopsis thaliana	Alpha-amylase 3, chloroplastic	61.179%	Swiss-Prot	moderate database homology
`Q8LFG1`	Arabidopsis thaliana	Probable alpha-amylase 2	54.787%	Swiss-Prot	moderate database homology
`A2YGY2`	Oryza sativa subsp. indica	Alpha-amylase isozyme 2A	51.444%	Swiss-Prot	moderate database homology
`Q0D9J1`	Oryza sativa subsp. japonica	Alpha-amylase isozyme 2A	51.444%	Swiss-Prot	moderate database homology

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