An expression database for roots of the model legume Medicago truncatula under salt stress

About us

The Medicago Truncatula Transporter database is a database of protein sequences of transporters of the model legume Medicago truncatula. The database is available to the public. Both automated search and manual curation were performed in identifying candidate protein sequences. Extensive annotations referring to each protein were generated, including basic protein function, genome locus, sequence annotations as well as transmembrane segment. A chromosome distribution map, text-based and BLAST search tools against known sequences of M.truncatula and known 3D structures of transporters were also created. A user-friendly web interface and regular updates make database valuable to researchers in related fields.

News

2012/9/7:The sever is not stable due to the electric power system's fault. Checking the problems is going to take a while, please bear with us.

2011/11/24 :The sever is not stable due to the electric power system's fault. Checking the problems is going to take a while, please bear with us.

2011/8/4 :The sever is not stable due to the electric power system's fault. Checking the problems is going to take a while, please bear with us.

2010/4/10: Database search available

2011/3/3: Database updata available

Abilities

Fucntions of pages listed below:

1.Home Page: this page. A brief introduction of this site

2.Search:A keywordbased text search is available for users to search by criteria such as transporter type, transporter family, transporter protein name or MtID.

3.Blast:Users can submit a single protein or DNA sequence in the ‘Blast’ section.

4.Browse:Users can browse the database by selecting the Transporter Type from drop-down boxes on the left of the web page.

5.Distribution map:The distribution map presents the locations of transporter genes. Genes are represented by squares and color coded according to their types. Clicking any block will redirect to the corresponding individual protein page.

6.Advanced Tools:Expression annotations, transmembrene segment and 3D structure can also be browsed quickly through the ‘Advanced Tools’ function

7.FAQ:FAQ page contains contents of common questions of and how to use MTDB.

Currently used data sources

1.Consensus sequences of Medicago truncatula probe sets: Affymetrix

2.Tentative Consensus sequences (TCs) of Medicago truncatula (Release 10.0): Medicago Gene Index

3.Protein/CDS/Unspliced transcript/Spliced transcript sequences of Medicago truncatula (Mt3.5 release):Medicago Genome Sequence Consortium (MGSC)

4.Genome sequences of Medicago truncatula (Mt3.5 release):Medicago Genome Sequence Consortium (MGSC)

5.Transporter sequences of Arabidopsis thaliana:TransportDB

6.Membrane transport proteins:Transporter Classification (TC) system

Other tools and data sources

1.BLAST: for multiple alignment and mapping predicted transporters onto the Affymetrix Medicago GeneChip

2.HMMTOP/TMHMM: for prediction of transmembrane helices and topology of protein

3.Pfam: for domain analysis

4.GenomePixelizer: for visualizing the gene distribution on chromosomes

5.Transporter annotations based on IMGAG V3.5 V3/M.truncatula Illumina RNA-Seq based gene models/MtGI:Noble Foundation

6.Microarray experiment data:MtED

7.Open Flash Chart: an open source software can generate very nice graph for many use.

8.FFAS03: for 3D-structure templates searching .

Cite MTDB

Miao Z, Li D, Zhang Z, Dong J, Su Z, Wang T. Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters. BMC Genomics. 2012 Feb 6;13(1):60. [PubMed]