LXL04_025209 | RubberDandelionOmics

Gene overview

LXL04_025209

Reference: OH-1004 Chr: Chr05 Coordinates: 107602827-107606983 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2697 bp · LXL04_025209|LXL04_025209|OH1004|cDNA

ATGGCGACGGTTCCTCTCGGGACGCATTTCTACCATTGTTGTCCCTCTGAAAGCCCTAAATTCCGTATAATTTCCAGAAAATATAAACGATCTTCGTTGCATGACAGTAGGAAAGGGAGTTTTATGGTAAAAACTGGCGCCAAAAGCTGCAAGTTCGGACAATCTTTTGATTGTAGGATTCTGTCCACCACCGTCAGAGCTTCTTCTAGTACCTCCATCTCGGACGCAGCTGTCCTTGACGCAGCCGTGTCCGATGACGT...

CDS

Download CDS FASTA

2697 bp · LXL04_025209|LXL04_025209|OH1004|CDS

ATGGCGACGGTTCCTCTCGGGACGCATTTCTACCATTGTTGTCCCTCTGAAAGCCCTAAATTCCGTATAATTTCCAGAAAATATAAACGATCTTCGTTGCATGACAGTAGGAAAGGGAGTTTTATGGTAAAAACTGGCGCCAAAAGCTGCAAGTTCGGACAATCTTTTGATTGTAGGATTCTGTCCACCACCGTCAGAGCTTCTTCTAGTACCTCCATCTCGGACGCAGCTGTCCTTGACGCAGCCGTGTCCGATGACGT...

Protein

Download Protein FASTA

898 aa · LXL04_025209|LXL04_025209|OH1004|PROTEIN

MATVPLGTHFYHCCPSESPKFRIISRKYKRSSLHDSRKGSFMVKTGAKSCKFGQSFDCRILSTTVRASSSTSISDAAVLDAAVSDDVIYRETFPLQRIEKVEGKISIRLDSGKDEENWQLTIGCNLPGKWVLHWGVNYENDPDSEWDQPPVDMIPQDSITIKDYAIQTPFTKSSTDSIYEVKIDFNTKSSIAAINFVLKDEETGSWYQYRGRDFKVPLVDFSLDYNNAVATKQGFAIWPGTSGQLSGTLVKSEDSLSENE...

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_025209`
TK1151 ID	TkA06G075210
OH-1004 ID	LXL04_025209
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.200
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_025209

Location Chr05:107602827-107606983 (-)

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
`Os08g0473600`	Important for breakdown of endosperm starch during germination.	No verified direct reference in this release
`Os09g0457600`	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_025209 · 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: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:Os09g0457500

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.

Plastid0.965

Rank 1 · LXL04_025209 · OH-1004

Mitochondrion0.038

Rank 2 · LXL04_025209 · OH-1004

Cytoplasm0.036

Rank 3 · LXL04_025209 · OH-1004

Peroxisome0.026

Rank 4 · LXL04_025209 · OH-1004

Nucleus0.025

Rank 5 · LXL04_025209 · 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.

PF23166.2Ig_N_CWD1100-218 aa

PF23166.2Ig_N_CWD1282-401 aa

PF00128.32Alpha-amylase528-603 aa

PF07821.19Alpha-amyl_C2839-896 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025209	`PF23166.2`	Ig_N_CWD1	100	218	2e-66	222.4
LXL04_025209	`PF23166.2`	Ig_N_CWD1	282	401	2e-66	222.4
LXL04_025209	`PF00128.32`	Alpha-amylase	528	603	8.6e-18	65.4
LXL04_025209	`PF07821.19`	Alpha-amyl_C2	839	896	5.3e-23	81.8

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	62.472%	Swiss-Prot	strong database homology
`Q8LFG1`	Arabidopsis thaliana	Probable alpha-amylase 2	51.010%	Swiss-Prot	weak database homology
`P27934`	Oryza sativa subsp. japonica	Alpha-amylase isozyme 3E	49.000%	Swiss-Prot	weak database homology
`P27937`	Oryza sativa subsp. japonica	Alpha-amylase isozyme 3B	48.507%	Swiss-Prot	weak database homology

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