Prefered browser : Internet Explorer 11 & Firefox 23.0.1 and above
logo_palmXplore
Malaysia MPIC MPOB

Welcome to PalmXplore

PalmXplore is a public-domain archive of predicted oil palm ( Elaeis guineensis ) genes. The database presently contains 26,059 high confidence oil palm genes generated by integrating two gene-prediction pipelines: FGENESH++ developed by Softberry and Seqping by MPOB.

Genome assembly and gene models are available for download here OR at the Genomsawit website.
| | | | | | | | |

 Please cite us!

Chan K-L, T Tatarinova, Rozana R, Nadzirah A, Azizi N, Mohd Amin A H, Nik Shazana N M S, Jayanthi N, Petr Ponomarenko, Martin Triska, V Solovyev, M Firdaus-Raih, Ravigadevi S, D Murphy and Low E T L. Evidence-based gene models for structural and functional annotations of the oil palm genome.

Quick Links

Advanced Search
Search by Scaffold ID, gene name, location on the chromosomes, functional annotation, Enzyme Code, GO, PFAM, etc. Options could be combined to provide for more descriptive results

CDS Browser
Browse the list of predicted gene identifiers (CDS ID)

Scaffold Browser
Browse the list of genomic scaffolds from E. guineensis P5-build assembly

MYPalmViewer
Explore and navigate the chromosomes of oil palm, it's annotations, and associated data tracks

BLAST
The integrated BLAST tool provides BLASTn, BLASTx, tBLASTx and tBLASTn programs to match a query sequence to oil palm gene sequences

Download
Download genome assemblies and gene annotation


Oil Palm Genome Statistics

Genome size 1.8 Gb
Total number of scaffolds40,360
Average / N50 / largest scaffold sizes (bp)38,036 / 1,045,414 / 22,100,610
Number of bases (bp)1,535,150,282

Representative Oil Palm Gene Models

Number of genes26,059
Average length (bp)1,239
Gene density (gene/Mb)16.98
Average exon per gene5.4
Average exon length (bp)252
Number of genes annotated with Gene Ontology term(s)21,572
Number of genes with Enzyme Code (KEGG)6,195
Data Available
VersionTotal
Pisifera genome buildP540,360 scaffolds
E. guineensis genome buildEG5.116 chromosomes
Gene modelEG5.1_Genes_V326,059 genes
Fgenesh++ predicted genes27,915 genes
Seqping predicted genes17,680 genes
Intronless genes3,658 genes
Resistance (R) genes210 genes
Fatty Acid Biosynthesis (FAB) genes42 genes

Chan et al., 2017

Distribution of oil palm gene models. a) Number of genes vs. number of exons per gene b) Number of genes vs lengths of CDS

Oil palm genes classification based on Gene Ontology annotation