LXL04_028894 | RubberDandelionOmics

Gene overview

LXL04_028894

Reference: OH-1004 Chr: Chr06 Coordinates: 73684614-73689067 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1620 bp · LXL04_028894|LXL04_028894|OH1004|cDNA

ATGGAAATGTCGTTGATTGCAAGATCTCCGGCGATCGGAAGAGATCTTTTTCAATTGAGAAATAATTATAACAACACTAATCTGATGTTTCTCTCTTCATCCGCCACCAAGTCGCAGATGGGTTTCCTTCAAACAAGATACCCTAATCTTCATCTTAAGGTTACTGCTCGATCTCTTTCTCATTCTCAGCCTGCTGCCTCCACCGAGCCTTCGTATGAGAACACGATTACCAGTCCCAAAGATGGAGTGAAGTTATACGT...

CDS

Download CDS FASTA

1620 bp · LXL04_028894|LXL04_028894|OH1004|CDS

ATGGAAATGTCGTTGATTGCAAGATCTCCGGCGATCGGAAGAGATCTTTTTCAATTGAGAAATAATTATAACAACACTAATCTGATGTTTCTCTCTTCATCCGCCACCAAGTCGCAGATGGGTTTCCTTCAAACAAGATACCCTAATCTTCATCTTAAGGTTACTGCTCGATCTCTTTCTCATTCTCAGCCTGCTGCCTCCACCGAGCCTTCGTATGAGAACACGATTACCAGTCCCAAAGATGGAGTGAAGTTATACGT...

Protein

Download Protein FASTA

539 aa · LXL04_028894|LXL04_028894|OH1004|PROTEIN

MEMSLIARSPAIGRDLFQLRNNYNNTNLMFLSSSATKSQMGFLQTRYPNLHLKVTARSLSHSQPAASTEPSYENTITSPKDGVKLYVGLPMNSVSDCHAINHSRAISAGLRALKLLGVEGVELPIWWGVVEKEAMGKYEWSGYRTLVEMIQKAGLKLHVSLCFHGCKQENIPLPRWVSELGKSEPDIFFADRSGKRYKDCLSFGIDDLPVFDGKTAMNVYQGFAESFKTSFSSFMGSTITGITIGMGPDGELRYPSHQEQ...

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_028894`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_028894

Location Chr06:73684614-73689067 (+)

Description Similar to BAM9: Inactive beta-amylase 9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g18670`	Inactive beta-amylase 9.	No verified direct reference in this release
`At4g17090`	Beta-amylase activity.	RNA interference of Arabidopsis beta-amylase8 prevents maltose accumulation upon cold shock and increases sensitivity of PSII photochemical efficiency to freezing stress.2005 · DOI: 10.1111/j.1365-313x.2005.02565.x Glucan, water dikinase activity stimulates breakdown of starch granules by plastidial beta-amylases.2007 · DOI: 10.1104/pp.107.104224
`At3g23920`	Beta-amylase activity.	Glucan, water dikinase activity stimulates breakdown of starch granules by plastidial beta-amylases.2007 · DOI: 10.1104/pp.107.104224
`At5g55700`	No alpha-1,4-glucan hydrolase activity, including beta-amylase, alpha-amylase, a-glucosidase or alpha-amyloglucosidase.	Beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in Arabidopsis chloroplasts.2008 · DOI: 10.1105/tpc.107.056507 Catalytically-inactive beta-amylase BAM4 required for starch breakdown in Arabidopsis leaves is a starch-binding-protein.2009 · DOI: 10.1016/j.abb.2009.07.024

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0141200`	Possesses beta-amylase activity in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028894 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000024 maltose biosynthetic process Biological Process

GO:0005983 starch catabolic process Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0016161 beta-amylase activity Molecular Function

KEGG gene cross-reference

ath:AT3G23920

ath:AT4G17090

ath:AT5G18670

ath:AT5G55700

dosa:Os03g0141200

osa:4331577

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Plastid0.932

Rank 1 · LXL04_028894 · OH-1004

Mitochondrion0.062

Rank 2 · LXL04_028894 · OH-1004

Nucleus0.043

Rank 3 · LXL04_028894 · OH-1004

Cytoplasm0.031

Rank 4 · LXL04_028894 · OH-1004

Peroxisome0.019

Rank 5 · LXL04_028894 · 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.

PF01373.25Glyco_hydro_1487-499 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028894	`PF01373.25`	Glyco_hydro_14	87	499	2.2e-98	330.8

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
`Q8VYW2`	Arabidopsis thaliana	Inactive beta-amylase 9	54.930%	Swiss-Prot	strong database homology
`O23553`	Arabidopsis thaliana	Beta-amylase 3, chloroplastic	40.281%	Swiss-Prot	moderate database homology
`Q9LIR6`	Arabidopsis thaliana	Beta-amylase 1, chloroplastic	38.495%	Swiss-Prot	moderate database homology
`Q9FM68`	Arabidopsis thaliana	Inactive beta-amylase 4, chloroplastic	37.416%	Swiss-Prot	moderate database homology
`Q10RZ1`	Oryza sativa subsp. japonica	Beta-amylase 2, chloroplastic	39.261%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card