LXL04_029288 | RubberDandelionOmics

Gene overview

LXL04_029288

Reference: OH-1004 Chr: Chr06 Coordinates: 86214443-86223750 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2712 bp · LXL04_029288|LXL04_029288|OH1004|cDNA

ATGAGTCGAATTGAGAGGCTCTTGAGGGAAAAAGAACTAAGAAAGAACAATAAAGCTTCCCATTCCAATGAATATATTGATCTTGAACCACGAGATGGATCCGAAGGTGATGGCAATATGAAAGAATATCTCAAAAAAGACTCTTTAGCAAGTGAAGGGTGTGAAAAACATGATGAAGGGCTGTTTAAAGAAAGGCTATTAGTCGTTGCTAATAGACTTCCGGTCTCTGCTGTTAGGACAGGTGAAGAGAGTTGGTCGCT...

CDS

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2712 bp · LXL04_029288|LXL04_029288|OH1004|CDS

ATGAGTCGAATTGAGAGGCTCTTGAGGGAAAAAGAACTAAGAAAGAACAATAAAGCTTCCCATTCCAATGAATATATTGATCTTGAACCACGAGATGGATCCGAAGGTGATGGCAATATGAAAGAATATCTCAAAAAAGACTCTTTAGCAAGTGAAGGGTGTGAAAAACATGATGAAGGGCTGTTTAAAGAAAGGCTATTAGTCGTTGCTAATAGACTTCCGGTCTCTGCTGTTAGGACAGGTGAAGAGAGTTGGTCGCT...

Protein

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903 aa · LXL04_029288|LXL04_029288|OH1004|PROTEIN

MSRIERLLREKELRKNNKASHSNEYIDLEPRDGSEGDGNMKEYLKKDSLASEGCEKHDEGLFKERLLVVANRLPVSAVRTGEESWSLEVRDGEHVTALLNVKEIEVKWIGWIGLHVPDERGQSSLIKALAHKRCIPVFLDEETIHQYYNGYCNNILWPLFHYLGLPQEDRLATTRTYESQFSAYKKANQMFADVVNLNYEEGDAVWCHDYHLMFLPKCLKDYNKNMKVGWFLHTPFPSSEIHRTLPSRSELLRAVLAADL...

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_029288`
TK1151 ID	TkA07G297150
OH-1004 ID	LXL04_029288
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	96.000
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

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Basic Information and Functional Annotation

Gene ID LXL04_029288

Location Chr06:86214443-86223750 (-)

Description Similar to TPS1: Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g78580`	Required for normal embryo development, vegetative growth and transition to flowering.	Trehalose metabolism in Arabidopsis: occurrence of trehalose and molecular cloning and characterization of trehalose-6-phosphate synthase homologues.2001 · DOI: 10.1093/jexbot/52.362.1817 Trehalose-6-phosphate synthase 1, which catalyses the first step in trehalose synthesis, is essential for Arabidopsis embryo maturation.2002 · DOI: 10.1046/j.1365-313x.2002.01220.x Truncation of Arabidopsis thaliana and Selaginella lepidophylla trehalose-6-phosphate synthase unlocks high catalytic activity and supports high trehalose levels on expression in yeast.2002 · DOI: 10.1042/bj20020517 Trehalose 6-phosphate is indispensable for carbohydrate utilization and growth in Arabidopsis thaliana.2003 · DOI: 10.1073/pnas.1132018100 Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering.2004 · DOI: 10.1104/pp.104.039743 Trehalose metabolism and glucose sensing in plants.2005 · DOI: 10.1042/bst0330276 The role of trehalose-6-phosphate synthase in Arabidopsis embryo development.2005 · DOI: 10.1042/bst0330280 Delayed embryo development in the ARABIDOPSIS TREHALOSE-6-PHOSPHATE SYNTHASE 1 mutant is associated with altered cell wall structure, decreased cell division and starch accumulation.2006 · DOI: 10.1111/j.1365-313x.2006.02662.x Isolation and molecular characterization of the Arabidopsis TPS1 gene, encoding trehalose-6-phosphate synthase.1998 · DOI: 10.1046/j.1365-313x.1998.00063.x
`At1g16980`	Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 2.	No verified direct reference in this release
`At4g27550`	Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 4.	No verified direct reference in this release
`At1g17000`	Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 3.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029288 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005991 trehalose metabolic process Biological Process

GO:0005992 trehalose biosynthetic process Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009832 plant-type cell wall biogenesis Biological Process

GO:0010182 sugar mediated signaling pathway Biological Process

GO:0046686 response to cadmium ion Biological Process

GO:0048364 root development Biological Process

GO:0048574 long-day photoperiodism, flowering Biological Process

GO:0051301 cell division Biological Process

GO:0080186 developmental vegetative growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G16980

ath:AT1G17000

ath:AT1G78580

ath:AT4G27550

ddi:DDB_G0287657

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.

Cytoplasm0.554

Rank 1 · LXL04_029288 · OH-1004

Nucleus0.283

Rank 2 · LXL04_029288 · OH-1004

Cell membrane0.096

Rank 3 · LXL04_029288 · OH-1004

Golgi apparatus0.077

Rank 4 · LXL04_029288 · OH-1004

Mitochondrion0.076

Rank 5 · LXL04_029288 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00982.28Glyco_transf_2065-527 aa

PF02358.23Trehalose_PPase597-818 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029288	`PF00982.28`	Glyco_transf_20	65	527	2.6e-177	591.0
LXL04_029288	`PF02358.23`	Trehalose_PPase	597	818	7.2e-56	189.6

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
`Q9SYM4`	Arabidopsis thaliana	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 1	68.630%	Swiss-Prot	strong database homology
`Q9FZ57`	Arabidopsis thaliana	Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 2	61.989%	Swiss-Prot	strong database homology
`Q9T079`	Arabidopsis thaliana	Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 4	56.235%	Swiss-Prot	strong database homology
`Q9SHG0`	Arabidopsis thaliana	Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 3	55.131%	Swiss-Prot	strong database homology

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