Database Structure

The major components of current Codex include three tables: gene table, hairpin table, and mature product table. The gene table lists all gene related information, such NCBI entrez gene IDs, HGNC gene symbol, alias gene name, associated transcript IDs, etc. The hairpin table lists all designed 21-mer for each genes in each species. The mature product table lists the information of shRNA constructs for all 21-mer designed. (See figure below).

Database Statistics

Current database includes shRNAs from four species: human, mouse, rat and fruit fly. The number of shRNAs and genes in each species are listed in the table below:

Species (genome version)Number of genesNumber of shRNAs
Human (build 36.1)57,293395,830
Mouse (build 37)80,113390,941
Rat (version 3.4)44,614269,508
Fruit fly (release 5)22,86381,410
Arabidopsis7,4738,868

shRNA constructs

We construct the shRNA for each 21-mer by using human-mir-30 loop to link guide and passenger strands of 21-mer. For drosophila construct, we use mir-1 loop instead. We also add primer sequences at each side of the construct for cloning and PCR amplification. For some constructs, 25-bp to 60-bp barcode sequences are also included to facilitate the screening. The example of construct is displayed below:

Database search

Users could search the database for shRNAs based on the information of their interested genes, such as:

Users can get shRNA information displayed on screen or batch-download shRNAs with a list of query genes.