R498 Summary
Statistics of the functionally annotated genes in R498
| Type | R498 |
| Gene number | 38,714 |
| Gene length | 2,292/3,012 |
| Transcript length | 1,296/1,480 |
| Max cds length | 14,214 |
| CDS length | 765/996 |
| Protein length | 254/331 |
| Exon length | 183/342 |
| Intron length | 152/419 |
| 5' UTR length | 116/211 |
| 3' UTR length | 274/340 |
| Exon number | 2.0/4.3 |
| Intron number | 1.0/3.3 |
* Each number indicates the median/average
Genome Browser
2 tracks of annotationBLAST
Online Blast R498/MSUDownload:
R498 Genome sequence(CANU)R498 Genome sequence(HERA)
R498 Genome sequence(soft mask)
Gene Anotation
Gene Anotation V3
Coreset Gene mRNA V3
Coreset Gene CDS V3
Coreset Gene Protein V3
Coreset Gene GO V3
Coreset Gene Pathway V3
R498 BioNano Raw Data
R498 Chromesome GeneticsMap
R498 Repeat Annotation
Updates
Nov. 23, 2018
– add MSU Annotation to R498(V3).
May 18, 2018
– add Repeat Annotation of R498.
Jan 3, 2018
– add Chromesome Gentics Map of R498.
Nov 24, 2017
– add new version(V3) of gene annotation for R498.
May 23, 2017
– add online blastfor R498/MSU.
May 4, 2017
– A paper describing the ShuHui498(R498) genome project has been published.
Introduction to R498 Genome Project
A high quality reference genome would enable discovery of genome structure and genetic variation. Here we report an integrative method to generate a 390.3-megabase assembly covering over 99% of the indica rice genome Shuhui498 with 7 of the 12 chromosomes complete and the rest 5 each containing only one gap in its centromeric region. Besides, we also identify important genome features and genetic variations among sequenced rice genomes.
We predicted 38,714 high confidence protein coding genes in R498 through an evidence-based gene prediction pipeline by combining known proteins, experimentally cloned cDNAs/ESTs and assembled transcripts from rice RNA-seq data.
This website provides genome sequence and gene annotation files of the indica rice genome(R498).
Basic genome statistics of R498
| Chrome | Length | N Gaps | Telomere |
| Chr1 | 44,361,539 | 1 | Both |
| Chr2 | 37,764,328 | 1 | Both |
| Chr3 | 39,691,490 | 1 | Both |
| Chr4 | 35,849,732 | 0 | Both |
| Chr5 | 31,237,231 | 0 | Both |
| Chr6 | 32,465,040 | 0 | Both |
| Chr7 | 30,277,827 | 1 | Both |
| Chr8 | 29,952,003 | 0 | Both |
| Chr9 | 24,760,661 | 0 | Both |
| Chr10 | 25,582,588 | 0 | Both |
| Chr11 | 31,778,392 | 1 | Both |
| Chr12 | 26,601,357 | 0 | Both |
| mtDNA | 527,116 | 0 | - |
| cpDNA | 134,546 | 0 | - |
| Total | 390,983,850 | 5 | 24 |
Cite
- Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li, Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li and Chengzhi Liang. Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications. DOI: 10.1038/ncomms15324 .