1️⃣ 序列获取(2)：RNA序列获取

序列比对和序列特征分析总目录

1 ncRNAdb(noncoding RNA database)

虽不编码蛋白质，但是参与包括染色质结构重建，基因表达层面的转录和翻译调控，亚细胞位置等调控。主要来自于

1 主要：ncRNAdb -- Noncoding regulatory RNAs database：通过以下方式获取

• Search search by organism name, RNA symbol or GenBank accession number

• BLAST BLAST your sequence against the ncRNAdb (over 30,000 sequences; 66,4 MB)

• Browse Information pages

• Download Download the sequences in FASTA format

2 哺乳动物RNAdb: mammalian noncoding RNA database

3 fRNAdb: functional RNA database

4 Rfam: database of noncoding RNA families

5 miRBase: microRNA database

• 可检索公开发表的miRNA序列和注释信息

• 可获得和下载miRNA的发卡和成熟序列
• 可下载miRBase中所有序列和注释
  -用户可以注册提交新miRNA,可命名
• 可以通过miRBase连接到microCom获取预测的靶基因
  ps，顺便安利一个关于miRNA的不错的网站tools4mirs

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.

6 tRNA database

7 UTRdb/UTRsite真核生物mRNA 5'和3'端非翻译区序列的非冗余数据库

The 5' and 3' untranslated regions of eukaryotic mRNAs play crucial roles in the posttranscriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. In the current update the UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets.

8 snoRNAbase: human H/ACA and C/D box snoRNA database

9 plant snoRNA database

10 yeast snoRNA database

11拟南芥ASRP: Arabidopsis thaliana small RNA project

12 tmRDB: database of tmRNA sequences

13 RNase P: RNase P RNA and protein database

14 SRPDB: Signal recognition particle database

15 methylation guide snoRNA database