LXL04_012577 | RubberDandelionOmics

Gene overview

LXL04_012577

Reference: OH-1004 Chr: Chr03 Coordinates: 14962946-14965253 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

582 bp · LXL04_012577|LXL04_012577|OH1004|cDNA

ATGAACACTATGTGCTTGGTATTTAGGACTTGGTTGGCGGGATATTTTAGGTCAAAAGGCGGAAGCGGGAAACGATTTTTGGTGTCAAAAGATAGAATTGGAGCATCAAGTTTGGAGTTTTTATACCGGCTTTTCAATTTTCAAGAAAAATCAGCAATCAAACATCTCCTTGGGTTCACCACTCATAATGATATTACTTACAGCATCTACAGAAGCTCCGTTCAAAGTTTACCAGAGATCGACGACTTTAAAGACGTGGA...

CDS

Download CDS FASTA

582 bp · LXL04_012577|LXL04_012577|OH1004|CDS

ATGAACACTATGTGCTTGGTATTTAGGACTTGGTTGGCGGGATATTTTAGGTCAAAAGGCGGAAGCGGGAAACGATTTTTGGTGTCAAAAGATAGAATTGGAGCATCAAGTTTGGAGTTTTTATACCGGCTTTTCAATTTTCAAGAAAAATCAGCAATCAAACATCTCCTTGGGTTCACCACTCATAATGATATTACTTACAGCATCTACAGAAGCTCCGTTCAAAGTTTACCAGAGATCGACGACTTTAAAGACGTGGA...

Protein

Download Protein FASTA

193 aa · LXL04_012577|LXL04_012577|OH1004|PROTEIN

MNTMCLVFRTWLAGYFRSKGGSGKRFLVSKDRIGASSLEFLYRLFNFQEKSAIKHLLGFTTHNDITYSIYRSSVQSLPEIDDFKDVDVELPAKATSATGSGFEILFQGFNWESNKSGRWYIELQEKIDELAALGFTVVWLPPPTESISPEGYMPRDLYNLNSRYGNVEELKALVKKFHQAGIRVLGDAVINHR

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_012577`
TK1151 ID	TkA03G586820
OH-1004 ID	LXL04_012577
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	98.600
Protein coverage (%)	TK1151 44.654 / OH-1004 36.788 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_012577

Location Chr03:14962946-14965253 (-)

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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0457400`	Important for breakdown of endosperm starch during germination.	No verified direct reference in this release
`Os08g0473600`	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_012577 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

GO:0005983 starch catabolic process Biological Process

GO:0005987 sucrose catabolic process Biological Process

GO:0005576 extracellular region 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

dosa:Os09g0457400

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.

Plastid0.969

Rank 1 · LXL04_012577 · OH-1004

Mitochondrion0.042

Rank 2 · LXL04_012577 · OH-1004

Cytoplasm0.040

Rank 3 · LXL04_012577 · OH-1004

Nucleus0.023

Rank 4 · LXL04_012577 · OH-1004

Peroxisome0.022

Rank 5 · LXL04_012577 · 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-amylase124-192 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012577	`PF00128.32`	Alpha-amylase	124	192	1.6e-14	54.6

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
`Q94A41`	Arabidopsis thaliana	Alpha-amylase 3, chloroplastic	68.992%	Swiss-Prot	moderate database homology
`P27932`	Oryza sativa subsp. japonica	Alpha-amylase isozyme 3A	54.839%	Swiss-Prot	weak database homology
`P27934`	Oryza sativa subsp. japonica	Alpha-amylase isozyme 3E	55.914%	Swiss-Prot	weak database homology

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