Transterm

Introduction

Welcome to Transterm! a database providing access to mRNA sequences and associated regulatory elements. A new feature (5/2015) is to analyse a human 3' UTR alignment to predict both protein and miRNA binding sites (go to Scan for Motifs).

The mRNA sequences are now processed from Refseq, including complete genomes. They are divided into biologically relevant sections 5' UTRs and 3' UTRs, initiation and termination regions and the full CDS sequences.

This data or your own sequences can be searched for defined regulatory elements (e.g. Puf3, Iron Responsive Element). The Transterm elements were updated here.

A more detailed overview is found in our publication "Transterm: a database to aid the analysis of regulatory sequences in mRNAs" in Nucleic Acids Research.

What can be done here?

Obtain data relating to translation, by species in a non-redundant format: for example bias around initiation and termination codons, or codon usage (more...).

Search for regulatory elements in a defined set - for example known or putative mRNA stability or localisation elements in 3'UTRs (more...).

Search your own sequence for known regulatory elements (more...).

Quick guide - how to use the database

This database contains data related to specific species and strains through NCBI TaxIDs, the initial default is Homo Sapiens (9606).

1) For the species many types of pre-processed data are available, differing in experimental support and redundancy. For completed genomes the most useful files are likely to be 'NCBI-Genomes - one sequence for each coding region' (more...)

2) Choose your TaxID species or strain (example...).

3) This data can be analysed for known or putative regulatory elements (more...). More about regulatory elements in mRNAs.

Alternative ways of using the database

Get descriptions of regulatory elements (example...).

Results

The results of your analysis will appear in a new tab or window (more...).

Species data:

Enter NCBI TaxID for species or strain:

Examples: 9606 H. sapiens

Database: Genomes-DB-CDS
Select RefSeq version:
Select sequence category:
Select data file:







Search own sequences for regulatory elements (Scan for Motifs)