Determine gene function for soyBean transcript

Question

[GreenDiamond]

I recently performed an RNA-sequencing analysis on soybean transcripts, and am interested in learning more about five transcripts of interest. In the transcript .fasta file, these transcript names are listed in the following format:

Glyma.18G057100.Wm82.a2.v1 Glyma.18G092200.Wm82.a2.v1 Glyma.09G164000.Wm82.a2.v1 Glyma.08G269900.Wm82.a2.v1 Glyma.07G079300.Wm82.a2.v1

I want to determine if there is a means to determine the tentative function of these transcripts? I have been looking through sites such as https://soybase.org/GlycineBlastPages/BlastSearch.php and https://david.ncifcrf.gov/, but have not had any success.

Any suggestions on how to perform this step would be much appreciated!

Answer 1

[lessismore]

I suggest to look at the gene level (not transcript) on https://plantcyc.org/

Answer 2

[GreenDiamond]

Thanks @lessismore. I am trying the site you recommended, but am still uncertain how to obtain tentative functions of these genes. I am sorry if it might be obvious! In the search bar at the type right, I selected "SoyCyc" in the left field and typed each of the five gene names I listed in my original post above one by one in the right field. For each one, it returned something like "No matches found for search string Glyma.18G092200.Wm82.a2.v1".

Do you believe this is the correct procedure? There are many options on the site you listed, and I would be grateful to hear your thoughts on what I tried! Thank you again.

[lessismore]

Hey @GreenDiamond im not expert in this but if you read here >> https://soybase.org/correspondence/ you'll see that the desinence "Wm82.a2.v1" means "Williams 82 assembly version 2 annotation version 1". The thing is that across the genome annotation versions your ID's may change. This results in not finding what you are searching for simply because your are searching with an outdated gene/transcript or whatever ID or viceversa you could be searching for something old with a new generated one. THats why on this page you have the correspondence table which allows you to recover what you are searching for across the genome annotation versions. Again citing the example in the link i gave you you have: For example, for Williams 82 assembly version 2 annotation version 1

Locus:     Glyma.01g000100
Locus ID:     Glyma.01g000100.Wm82.a2.v1
Transcript:     Glyma.01g000100.1
Transcript ID:     Glyma.01g000100.1.Wm82.a2.v1

From what ive seen they computationally transfer annotations. This is why of course the experimentally validated genes are a minimal part and generally come from Arabidopsis. Anyway if i go on Soybase https://www.soybase.org/ and i search in the SoyBase Toolbox the gene locus ID you are providing i find it >> https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&version=Glyma2.0&search_term=Glyma.18g092200

[GreenDiamond]

Thank you for your very helpful comment!

Answer 3

[theobroma22]

You could also easily Blast the corresponding sequences to get the gene level information.