RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

TkA08G040440
Reference: TK1151 Chr: Chr08 Coordinates: 10276721-10282423 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2741 bp · TkA08G040440|TK1151|cDNA

CGCCCCTAGATTTTTGTGAGGTTGAGGGTGATGTGGTATGGACGTTCGTGTTCTAACGTCCAACCCACCACACCTAATAGCGTAAGCCCTCTTCTCAGATCACACGTTCACTGAAACCCAAACCCCACATTCATCCTTAAACTTTCAGGCATCTCTGCTCACTACTGCCAGACTCCCCCGACTCGAATCTCGAAGGATTTATGGATGCTTCTGTGATGGAAAAACTACTTAGATGTGCTTCCTACTCTCCTCTCCACACT...

CDS

Download CDS FASTA

2391 bp · TkA08G040440|TK1151|CDS

ATGGATGCTTCTGTGATGGAAAAACTACTTAGATGTGCTTCCTACTCTCCTCTCCACACTCCTAAACTCACATCTACTCACAATTTTGAATTCCGAAATCCTAATATACATATGAAATGGCGTACTCGGAAGAACAACAATGCCGTAAATGCAAGCAAAGGAGGAGGTGGAGAAGTGGATACGGCGGTGGTGGAAAAGGACAAGCCGAAAGTACTGCCGCGGCGATTTCAGATTTTACAGGGTTCTCCGATGCCGTTTGG...

Protein

Download Protein FASTA

796 aa · TkA08G040440|TK1151|PROTEIN

MDASVMEKLLRCASYSPLHTPKLTSTHNFEFRNPNIHMKWRTRKNNNAVNASKGGGGEVDTAVVEKDKPKVLPRRFQILQGSPMPFGATAQEDGVNFAIYSRNATSATLCLMTPSDLPEKRITEQIPLDQLTNKTGDVWHVFLKGDFTDMLYGYKFSGDFSPEEGHYYDSSRILLDPYAKAVLSREEFGVLGPDDDCWSQMACKVPSNHEFDWEGDLPLSFAQRDLVIYEMHVRGFTRHESSKTESPGTYLGVVDKLDHL...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDTkA08G040440
TK1151 IDTkA08G040440
OH-1004 IDLXL04_017919
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.500
Protein coverage (%)TK1151 99.372 / OH-1004 81.884
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 versionTK1151 / GWHBCHF00000000
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDTkA08G040440
LocationChr08:10276721-10282423 (+)
DescriptionSimilar to ISA1: Isoamylase 1, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g39930 Involved in the trimming of pre-amylopectin chains. No verified direct reference in this release
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

Rice

Reference gene IDPossible functionPapers / DOI
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
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
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_017919 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Plastid0.931
Rank 1 · TkA08G040440 · TK1151
Cytoplasm0.067
Rank 2 · TkA08G040440 · TK1151
Mitochondrion0.050
Rank 3 · TkA08G040440 · TK1151
Peroxisome0.037
Rank 4 · TkA08G040440 · TK1151
Cell membrane0.037
Rank 5 · TkA08G040440 · TK1151

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.

PF02922CBM_4885-179 aa
PF02922CBM_48190-235 aa
PF00128Alpha-amylase239-352 aa
PF02638GHL10325-418 aa
PF00128Alpha-amylase387-434 aa
PF00128Alpha-amylase593-640 aa
PF21156ISOA1-3_C683-786 aa
PF02922CBM_48683-705 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA08G040440PF02922CBM_48851791.5e-1764.4
TkA08G040440PF02922CBM_481902351.5e-1764.4
TkA08G040440PF00128Alpha-amylase2393528.5e-2175.4
TkA08G040440PF02638GHL103254180.1112.3
TkA08G040440PF00128Alpha-amylase3874348.5e-2175.4
TkA08G040440PF00128Alpha-amylase5936408.5e-2175.4
TkA08G040440PF21156ISOA1-3_C6837862.6e-48163.3
TkA08G040440PF02922CBM_486837051.5e-1764.4

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
O04196Arabidopsis thalianasp|O04196|ISOA1_ARATH Isoamylase 1, chloroplastic72.100%Swiss-ProtHigh
Q9M0S5Arabidopsis thalianasp|Q9M0S5|ISOA3_ARATH Isoamylase 3, chloroplastic46.400%Swiss-ProtMedium
D0TZF0Oryza sativa subsp. japonicasp|D0TZF0|ISOA1_ORYSJ Isoamylase 1, chloroplastic71.000%Swiss-ProtHigh
B9G434Oryza sativa subsp. japonicasp|B9G434|ISOA3_ORYSJ Isoamylase 3, chloroplastic46.800%Swiss-ProtMedium

JBrowse

View in Genome Browser