different transcripts show hits to same gene but in different species, what is it showing?
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7.2 years ago
Farbod ★ 3.4k

Hi, I have collect several genes of interest in a fasta file and blastn them (e-value=1e-6) against my species of interest transcriptome (RNA-seq assembly using Trinity) blastable database.

I have same genes for different species in my genes collection. e.g Human Gh (growth hormone), zebrafish Gh, pufferfish Gh. and I have collect them from NCBI nucleotide section.

Now I have different Trinity transcripts aligned with each of them separately. e.g:

TRINITY_DN105473_c4_g1_i3 -----------------------------------------> Human GH

TRINITY_DN101371_c3_g1_i2 ----------------------------------------> Zebrafish Gh

TRINITY_DN158974_c0_g1_i1 ----------------------------------------> puffer fish Gh

what is it showing ? Are these transcripts Orthologus or Paralogous ? or someting else and how I can become sure about it?

(I must mention that in most cases there is vice versa , I mean all the different species similar genes will show homology to just one transcript. e.g: TRINITY_DN103130_c0_g1_i1 ----------------------- > Human AR, Zebrafish Ar, Pufferfish AR )

blast alignment gene • 1.1k views

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