LXL04_026494 | RubberDandelionOmics

Gene overview

LXL04_026494

Reference: OH-1004 Chr: Chr05 Coordinates: 127347496-127350406 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1377 bp · LXL04_026494|LXL04_026494|OH1004|cDNA

ATGGCTCCTCAAAACGTTGGAATTCTCGCCATGGAAATCTACTTCCCTCCTACTTGTATCAAACAGGATACTCTAGAAAACTTTGATGGAGTCAGTAAAGGAAAATACACCATTGGACTCGGACAAGATTGCATGGCATTTTGCTCAGAGGTTGAAGATGTCATTTCCATGGGACTGACAGCTGTCACTTCACTACTCGAGAAGTATGAAATCGACCCAAAACAAATCGGTCGATTGGAAGTCGGGAGTGAAACCGTAAT...

CDS

Download CDS FASTA

1377 bp · LXL04_026494|LXL04_026494|OH1004|CDS

ATGGCTCCTCAAAACGTTGGAATTCTCGCCATGGAAATCTACTTCCCTCCTACTTGTATCAAACAGGATACTCTAGAAAACTTTGATGGAGTCAGTAAAGGAAAATACACCATTGGACTCGGACAAGATTGCATGGCATTTTGCTCAGAGGTTGAAGATGTCATTTCCATGGGACTGACAGCTGTCACTTCACTACTCGAGAAGTATGAAATCGACCCAAAACAAATCGGTCGATTGGAAGTCGGGAGTGAAACCGTAAT...

Protein

Download Protein FASTA

458 aa · LXL04_026494|LXL04_026494|OH1004|PROTEIN

MAPQNVGILAMEIYFPPTCIKQDTLENFDGVSKGKYTIGLGQDCMAFCSEVEDVISMGLTAVTSLLEKYEIDPKQIGRLEVGSETVIDKSKSIKTFLMQIFEDCGNTDIEGVDSTNACYGGTAALFNCVNWVESSSWDGRYGLVVSTDSAVYAEGAARPTGGAGAVAMLIGPDAPIAFESKFRASHMEHVYDFYKPDLASEYPVVDGKLSQTCYLMALDSCYKRYCQKYEKIQGKEFSMADADYFVFHSPYNKLVQKSFA...

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_026494`
TK1151 ID	TkA06G008820
OH-1004 ID	LXL04_026494
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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_026494

Location Chr05:127347496-127350406 (+)

Description Similar to HMGS: Hydroxymethylglutaryl-CoA synthase

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g11820`	This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.	The Arabidopsis FLAKY POLLEN1 gene encodes a 3-hydroxy-3-methylglutaryl-coenzyme A synthase required for development of tapetum-specific organelles and fertility of pollen grains.2010 · DOI: 10.1093/pcp/pcq068

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026494 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006084 acetyl-CoA metabolic process Biological Process

GO:0006629 lipid metabolic process Biological Process

GO:0006695 cholesterol biosynthetic process Biological Process

GO:0010142 farnesyl diphosphate biosynthetic process, mevalonate pathway Biological Process

GO:0016126 sterol biosynthetic process Biological Process

GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway Biological Process

GO:0033386 geranylgeranyl diphosphate biosynthetic process Biological Process

GO:0033489 cholesterol biosynthetic process via desmosterol Biological Process

GO:0033490 cholesterol biosynthetic process via lathosterol Biological Process

GO:0036197 zymosterol biosynthetic process Biological Process

GO:0044351 macropinocytosis Biological Process

GO:0005654 nucleoplasm Cellular Component

KEGG gene cross-reference

ath:AT4G11820

ddi:DDB_G0288461

hsa:3157

pon:100174584

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.

Cytoplasm0.741

Rank 1 · LXL04_026494 · OH-1004

Nucleus0.273

Rank 2 · LXL04_026494 · OH-1004

Endoplasmic reticulum0.102

Rank 3 · LXL04_026494 · OH-1004

Mitochondrion0.074

Rank 4 · LXL04_026494 · OH-1004

Cell membrane0.061

Rank 5 · LXL04_026494 · 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.

PF01154.23HMG_CoA_synt_N3-175 aa

PF08540.17HMG_CoA_synt_C176-450 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026494	`PF01154.23`	HMG_CoA_synt_N	3	175	1e-84	283.4
LXL04_026494	`PF08540.17`	HMG_CoA_synt_C	176	450	3.9e-110	368.6

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
`P54873`	Arabidopsis thaliana	Hydroxymethylglutaryl-CoA synthase	76.035%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card