Where can I find annotation of a wheat Unigene Build?

Question

[anna.gordon]

Hi there,

A bit of a basic question, I've used the latest Wheat (Triticum aestivum) Unigene build 63 as my "reference" genome to map Illumina single end sequences to so I can perform differential expression analyses. Each unique gene ID has this format eg: Ta_S61633485

I'm shocked that there seems to be no central repository for any accompanying GO annotation. There MUST be some somewhere surely? If you work on wheat and you know the answer, can you please please give me a pointer??

I've tried FAQs at plantdb, NCBI, cerealsdb, INRA, GrainGenes

Many thanks,
Anna

[BDK_compbio]

I am not sure if this will help ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/

[komal.rathi]

I don't think it will. That's a fasta file, not an annotation file.

Answer 1

[komal.rathi]

Have you looked at dbWFA (wheat functional annotation)? Check this link and click on Transcript(s) annotation on the bottom left panel. You can paste your list of gene IDs and get the corresponding GO annotation. I just saw the latest annotations they have is for build #62. But I guess, it may not be very different between #62 & #63.

[anna.gordon]

Hi there,

Many thanks for pointing that part of the page out to me - I hadn't spotted it. Unfortunately my gene IDs are returning "Transcript ID was not found" or "No hit" possibly because I've used a later Unigene build, but I'll email them directly to see if they've got some ideas..

Cheers,
Anna

Ta_S12857639
Ta_S12857704
Ta_S12858073
Ta_S12858139
Ta_S12858143
Ta_S12858227
Ta_S12858389
Ta_S12858483
Ta_S12858490
Ta_S12858540