LXL04_039111 | RubberDandelionOmics

Gene overview

LXL04_039111

Reference: OH-1004 Chr: Chr09 Coordinates: 59462494-59470592 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2676 bp · LXL04_039111|LXL04_039111|OH1004|cDNA

ATGATACACGTGACTGGCTCAAAAGAGTCACGTCCTCACGTGGCAGACATGAAAAAGACGTTGTCCCGCTTCTATGCCTGGAATCACTATGCATTTTGTCCTGATGCTCAACTTCATTCGATGCTTAGCGTGAAGAACATAATGATTCTCAACATAGCAACTTCATGTCTTGATTCATCCTCAAAAATCAGTAATGTCAATCATTCTCTTCCTCTTTCTGCATTTCGCGCCACCGCGGCCATGGGAGTAATCTGGAGTAG...

CDS

Download CDS FASTA

2676 bp · LXL04_039111|LXL04_039111|OH1004|CDS

ATGATACACGTGACTGGCTCAAAAGAGTCACGTCCTCACGTGGCAGACATGAAAAAGACGTTGTCCCGCTTCTATGCCTGGAATCACTATGCATTTTGTCCTGATGCTCAACTTCATTCGATGCTTAGCGTGAAGAACATAATGATTCTCAACATAGCAACTTCATGTCTTGATTCATCCTCAAAAATCAGTAATGTCAATCATTCTCTTCCTCTTTCTGCATTTCGCGCCACCGCGGCCATGGGAGTAATCTGGAGTAG...

Protein

Download Protein FASTA

891 aa · LXL04_039111|LXL04_039111|OH1004|PROTEIN

MIHVTGSKESRPHVADMKKTLSRFYAWNHYAFCPDAQLHSMLSVKNIMILNIATSCLDSSSKISNVNHSLPLSAFRATAAMGVIWSRNASGKSYVSGFSGKVKGSDRMKHMSSYVHSKRAEEIVIQEEIPVMSESRLSLKSIPGLPNPLGVSETENGINFALFSKHATSVTLCLLLPDSNNASSNDDGMIELKLDPHANKTGDIWHICVEELPRSSVLYGYRIDGPQDWHQGHRFDSSVVLIDPYAKLTQGRRIFGQVSD...

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_039111`
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_039111

Location Chr09:59462494-59470592 (+)

Description Similar to ISA3: Isoamylase 3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g09020`	Involved in starch catabolism.	Evidence for distinct mechanisms of starch granule breakdown in plants.2006 · DOI: 10.1074/jbc.m513661200 Further evidence for the mandatory nature of polysaccharide debranching for the aggregation of semicrystalline starch and for overlapping functions of debranching enzymes in Arabidopsis leaves.2008 · DOI: 10.1104/pp.108.129379 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
`At2g39930`	Involved in the trimming of pre-amylopectin chains.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0469400`	Starch-debranching enzyme that plays a role in the degradation of transitory starch during the night in leaf blades, facilitates the formation of spherical amyloplasts containing compound granules in the endosperm, and affects morphological characteristics of plastids.	Rice debranching enzyme isoamylase3 facilitates starch metabolism and affects plastid morphogenesis.2011 · DOI: 10.1093/pcp/pcr058
`Os08g0520900`	Starch-debranching enzyme involved in amylopectin biosynthesis in endosperm.	Complementation of sugary-1 phenotype in rice endosperm with the wheat isoamylase1 gene supports a direct role for isoamylase1 in amylopectin biosynthesis.2005 · DOI: 10.1104/pp.104.051359 Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm.2006 · DOI: 10.1007/s00425-006-0331-z Functional diversity of isoamylase oligomers: the ISA1 homo-oligomer is essential for amylopectin biosynthesis in rice endosperm.2011 · DOI: 10.1104/pp.111.173435

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_039111 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005983 starch catabolic process Biological Process

GO:0009660 amyloplast organization Biological Process

GO:0010021 amylopectin biosynthetic process Biological Process

GO:0019252 starch biosynthetic process Biological Process

GO:0009501 amyloplast Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009569 chloroplast starch grain Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0010368 chloroplast isoamylase complex Cellular Component

GO:0043033 isoamylase complex Cellular Component

GO:0019156 isoamylase activity Molecular Function

KEGG gene cross-reference

ath:AT2G39930

ath:AT4G09020

dosa:Os08g0520900

dosa:Os09g0469400

zma:542318

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.

Plastid0.926

Rank 1 · LXL04_039111 · OH-1004

Cytoplasm0.064

Rank 2 · LXL04_039111 · OH-1004

Mitochondrion0.053

Rank 3 · LXL04_039111 · OH-1004

Peroxisome0.036

Rank 4 · LXL04_039111 · OH-1004

Cell membrane0.033

Rank 5 · LXL04_039111 · 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.

PF02922.25CBM_48148-246 aa

PF00128.32Alpha-amylase314-433 aa

PF21156.4ISOA1-3_C733-797 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039111	`PF02922.25`	CBM_48	148	246	7.9e-14	52.5
LXL04_039111	`PF00128.32`	Alpha-amylase	314	433	2.3e-18	67.4
LXL04_039111	`PF21156.4`	ISOA1-3_C	733	797	8.6e-13	49.1

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
`Q9M0S5`	Arabidopsis thaliana	Isoamylase 3, chloroplastic	73.943%	Swiss-Prot	strong database homology
`O04196`	Arabidopsis thaliana	Isoamylase 1, chloroplastic	45.634%	Swiss-Prot	moderate database homology
`B9G434`	Oryza sativa subsp. japonica	Isoamylase 3, chloroplastic	70.183%	Swiss-Prot	strong database homology
`D0TZF0`	Oryza sativa subsp. japonica	Isoamylase 1, chloroplastic	47.384%	Swiss-Prot	moderate database homology

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