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 annotation


Online Blast R498/MSU


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


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


  • 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 .