the following link could interested you

http://pure.au.dk/portal/en/publications/wheat-ferritins-improving-the-iron-content-of-the-wheat-grain%2831473087-a19b-439b-8905-bbf350536249%29.html

you can try to contact directly the author through the link

https://www.researchgate.net/publication/257239224_Wheat_ferritins_Improving_the_iron_content_of_the_wheat_grain

Article Wheat ferritins: Improving the iron content of the wheat grain

do you have the whole genome the organism? if not what i can suggest is that remapped the gene back to close relative plant genome from there you can try design primer and amplified your wheat and do sequencing from there you can target the expected intron and exon  

Simply if you blast your RNA seq. on the NCBI website it will provide you with multiple hits including the genomic seq. and also it will tell you if this hit is a full gene or a full cDNA clone, or if it was BAC or PAC clone ... However, if it was only an STS... You by then need to design a primers based on your RNA seq. and isolate the gene by yourself and re-seq it. Another clue... Try to find the codons for TATA box, CAT box and splicing signals... If you got these in a seq. this means that you have a promoter and intron seq in your seq. which makes it a DNA... Because these sites are taken off during RNA splicing... Wish you all the best... And wish I understood your quest. in the right way... :)

Map raw sequencing data to your sequence of interest. Take the consensus of the reads. If you are missing some data repeat this until you get the full sequence.

Dear All thanks for your kind replies.

Actually I am designing gene specific genomic sequence based marker for metal binding proteins in wheat including ferritin, IRT, FRO, ZIP etc.

Dear Herve, thanks for your kind reply but ferritin is well studied iron storage protein in wheat and I am taking it as control, I have list of more than 25 genes responsible for metal uptake, transport, translocation and storage, where few of them are known in wheat while various are still not full characterized in wheat and there full sequences are not available in NCBI/EBI/URGI/IWGSC. 

Dear Ahmad Zaidi, Yes wheat genome raw sequence is available. but various genes are still not mapped in wheat genome. I had tried to design primer from cDNA or mRNA and amplified on wheat genomic DNA through PCR then out of 10 primer pairs only 2 showed amplification. The main reason behind this failure might be due to one of the primer pair contains sequence from the splice junction and unable to bind on genomic DNA sequence.

Dear Ahmad AlFatih, Thanks for your kind reply but I am not working on RNAseq,

In brief my strategy is like that:-

I had identified the sequence of various metal related genes (some are fully characterized in wheat wheat like ferritin while various genes are still not fully characterized in wheat like YS1, but full CDS sequence is available for Zea mays or rice). I had BLAST the sequence of gene (query sequence) with online available wheat genome sequence (raw reads- - Triticum aestivum -Ensembl Plants). From those genomic sequences I am planing to design the primer and amplify in wheat and wild relatives (The whole idea is to design gene specific genomic sequence based polymorphic marker which could be used in marker assisted selection for related to metal binding proteins including biofortification of wheat through molecular breeding). But I think there might be few flaws in my studies like sequence alignment (global) in between gene (query sequence) and raw reads (DNA sequence). Could I use specialized program or tool or any version of BLAST, which could help me.

Dear Rachel, Please tell me that how I can map raw sequencing data to my sequence of interest. Please specify tool, or pipeline or paper which could help me in this regards.

Thanks again and waiting for your kind reply.

Have a nice day 

Regards

Shailender

Map with bowtie2 - you can view with samtools tview and come up with the consensus manually. You can use our software GFR https://github.com/rachelss/GFR but it doesn't yet accommodate indels so I imagine it wouldn't give you the introns. If you program you can fork and edit it - then send me a pull request. I simply have not had the time to add this.

Dear Rachel,

  Thanks a lot for your kind suggestions and help. I am trying your suggestions and hope that it will definitely help me. If I face any problem then I will contact you.

Thanks again and all the best for your research.

With best regards

Shailender

I suggest you watch this tutorial. This is very simple. 

https://youtu.be/51qS-8F1sNg