The main goal of GRS_UTRdb is to predict the presence of Quadruplex forming G Rich
Sequences (QGRS) in the untranslated regions (UTRs) of eukaryotic mRNA sequences.
The search function contains the following user choices. Note: all searches are caseindependent.
The search function contains the following user choices. Note: all searches are caseindependent.
Organism:
At present, GRS_UTRdb contains information for two organisms: human and mouse.
The user may perform a search on either organism by itself or all organisms (which is the
default).
Search Field:
There are fourteen different fields that the user may search on.
Search Field
Gene ID
Gene Name
GI
Chromosome
Gene length
GO function
GO process
GO component
Organism
mRNA Accession #
mRNA length
5’ UTR length
CDS length
3’ UTR length
Comments
The unique identifier used in Entrez Gene
The official NCBI gene name. The user may search for
a gene having precisely this name, containing the
name, starting or ending with the name.
The unique identifier used in NCBI
Which chromosome the gene is located on
A range of values for the length of the gene
Gene ontology function
Gene ontology process
Gene ontology component
The user may perform a search on a particular set of
organisms or all organisms (which is the default).
NCBI accession number
A range of values for the length of the mRNA product
A range of values for the length of the 5’ UTR
A range of values for the length of the CDS
A range of values for the length of the 3’ UTR
Query results
Suppose we want to analyze human and mouse mRNA that come from genes that play a
role in RNA binding. Also suppose that we want to examine mRNA with fairly long 5'
and 3' UTRs. We could use the following search parameters
GO function: RNA binding
5' UTR length: 200 to 4000
3' UTR length: 200 to 4000
GRS_UTRdb Search Page
This results in 24 hits. Here is the first page of results. The results may be sorted using
any of the columns. For example, sorting by Gene Size sorts the genes in increasing order
of gene size.
GRS_UTRdb Results Page
To analyze a particular mRNA product one clicks on an entry in the Analyze mRNA
column. Suppose we select NM_001033049.1, which corresponds to the ADARB1
adenosine deaminase, RNA-specific gene. This then leads to a page entitled mRNA Map.
This page contains basic information about the product, the numbers of QGRS and gives
a visual map of the location of QGRS in the 5' UTR, the CDS, and the 3' UTR.
GRS_UTRdb mRNA Map
There are several ways of displaying data about QGRS. In the Data View, each QGRS is
listed together with its location in either the 5' or 3' UTR, or the CDS. Also, for QGRS
occurring in the 5' UTR the distance to the polyA signal and site is given.
GRS_UTRdb Data View
The Data View (with overlaps) gives a similar display, except that all QGRS, whether
overlapping or not, are given.
GRS_UTRdb Data View (with overlaps)
In the Sequence View, the location of QGRS are indicated in boxes, with each group of
G's highlighted in purple. This view can be selected for the full sequence, the 3' UTR, the
CDS, or 5' UTR.
GRS_UTRdb Sequence View
The Gene View gives basic information about the gene which the product was derived
from. This includes information about gene ontology. Also, there are tables giving QGRS
information for each product of the gene. The information about alternate products can
also be reached directly by the Alternate Products button at the top of each page.
GRS_UTRdb Gene View