Hippophae rhamnoides Information Archive
Hippophae rhamnoides Information Archive
- The sea buckthorn repeat sequences were identified using a combination of de novo and homology-based searches with Repbase v19.06. Protein-coding genes were predicted with homology-based, de novo, and transcript-based approaches. Noncoding RNA genes for miRNA, tRNA, and rRNA were predicted using de novo and/or homology search methods.
| Features | |
|---|---|
| Number of predicted protein-coding genes | 30,864 |
| Average gene length (bp) | 4,900 |
| Mean intron length (bp) | 3,153 |
| Annotated to KEGG | 11,251 |
| Annotated to GO | 18,518 |
| Annotated to KOG | 18,150 |
| Annotated to TrEMBL | 30,586 |
| Annotated to nr | 30,606 |
| Unannotated | 104 |
| tRNAs | 699 |
| rRNAs | 211 |
| miRNAs | 108 |
| Percentage of repeat sequences (%) | 67.81 |
References:
Xu, Z. & Wang, H. LTR_Finder: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic acids research 35, W265-W268 (2007).
Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110, 462-467 (2005).
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 27, 573-580 (1999).