This is how I would do it, hope you find it useful:
-Go to Phytozome database (www.phytozome.net).
-Select Species (Triticum aestivum).
-In the Species Info page, select Keyword Search.
-In the search box type "MYB". Click "GO"
-You will get a list of genes. Click on the "G" box to go to Gene View.
-Click on the menu tab "Sequences" and you'll get all the sequences you need (genomic, transcript, protein)
If you already have a partial sequences, you can also do BLAST to find the gene and get the whole sequence.
the missing part of cDNA can find using 3 or 5 RACE techniques also there is special kit from Biotech company for that. after getting the sequence you can compare the sequence with the genomic one through chromosome walking techniques
Gustavo Acevedo-Hernandez: I could not find wheat data in www.phytozome.net. It would be helpful if you could share a full link after choosing species name.
Thanks.
This is how I find genes in Wheat:
You can identify Genes in wheat using Wheat ENSEMBL database (http://plants.ensembl.org/Triticum_aestivum/Info/Index). If you already have a partial sequence of MYB genes then use that sequence as querry to BLAST against genomic sequence of Triticum aestivum in ENSEMBL. (if you don't have the sequence then retrieve the protein sequence from uniprot by putting gene name and plant name as keyword or from previously reported sequences in closest crop plant like Brachypodium or RIce). you will get all the homeologs of the genes in A,B and D genome. choose top three sequences on the basis of lowest e-value and highest bit score and retrieve the sequences from there. You will have the option whether you want CDS or cDNA or Amino Acid or Intron Exon and some more options are there. Further you may check the sequences by 3' / 5' RACE to be very sure that you have actually got the full length of the gene.
Hope that helps.
Anil Kumar: This is the link to Wheat data in Phytozome:
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Taestivum_er
- Badges
- Science topic
- Similar topics
- Biological Science
- Botany
- Plant Biology
- Plant Biotechnology