Plant miRNA SSR database [PmiRNASSRdb]
Tools for explore Micro-satellite associated miRNA in plants

Welcome to PmiRNASSRdb


Microsatellites or simple sequences repeat (SSRs) are frequently distributed in genes, intergenic regions and transposable elements in the genomes, they were identified and use for developing molecular markers in plant and animals. Recent studies demonstrated that SSR also be present in pre-microRNAs (miRNAs) sequences. But they are not well documented in plants.

To facilitated the wider use of SSR-associated plant miRNA, we constructed a user-friendly, freely accessible web-based, searchable and downloadable molecular marker database. This database encompasses 3573 miRNA-SSR markers along with its motif repeat, motif length, SSR class (Class I, Class II), motif type, motif nucleotide base composition (AT-rich, GC-rich, AT-GC balance), marker id, miRNA family, inslilico transferability, inslico polymorphic information. Marker information can retrieve by using a general search or customized search options (tools). General search tools facilitated to search miRNA-SSR markers information based on single search parameters viz., SSR Type; SSR Class; SSR Motif Rich with and miRNA family, etc. While customizing search tool allows to fish out more specific miRNA-SSR markers from the database using several parameters together in different combinations based on the user interest.

Peop1


db Info: PmiRNASSRdb: Version 1.

Current version of this database contains 3573 pre-miRNA-SSR markers from the 292 plant species of six plant taxa (Algae, Fungi, Bryophytes, Pteridophyte, Gynmosperm, Monocot and Dicot).


Database Search

A search returns of all the information on markers as a list in tabular format, including marker id, SSR motif, motif type, motif nucleotide base composition, primer sequences, annealing temperature, PCR product size, flanking sequences, miRNA family, transferability and polymorphism. Furthermore, the database provides a download facility for the search data. The database can be accessed via "Database Search" menu in the nevigation bar.


Results / summary





Frequency, Density and Distribution of Simple Sequence Repeats in pre-miRNA sequences:
A total of 16,892 pre-miRNA sequences from 292 plant species were searched for SSRs. The percentage of SSR-containing pre-miRNAs ranged from 38 for mosses and conifers to 84 for fungi. On average, at least 1.2 SSRs were found per plant, pre-miRNA sequence. Overall, 51% of plant pre-miRNA sequences contained at least one SSR. The SSR frequency and density gradually increased from lower to higher in the plant species. Class II (SSR length shorter than 20 bp) SSRs were more frequent than Class I (longer than 19 bp) SSRs in plant pre-miRNA sequences. [ more details ...]

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