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I have to check the expression of a gene in a fish whose sequence is not known in the fish in question. Sequence is known in an another fish (zebrafish) but the gene has 10 isoforms. The genome of fish in question is not sequenced, however RNA-seq data is available. I have no knowledge of RNA seq data analysis. Is it possible to know the sequence of gene of interest from this RNA-seq information?

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Okay, so you have RNASeq, but no reference genome for your fish? Just transcript sequence from zebrafish? Are you just trying to see if this gene is expressed, or you need to a more global view to compare it to?

If you just want to see if the gene is expressed, easy thing to do is to make a reference just made up of zebrafish transcripts, align to that. If there are too many differences between your fish and zebrafish, that won't work.

In which case, the next thing you could try is de novo assembly of your RNAseq data, then use blast to compare the zebrafish trasncripts to your assembled transcripts. Blast will make alignments where a short read aligner might not.

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Yes, it is possible, if the gene was expressed in the cells where the RNA was harvested from.

With RNA seq basically you sequence the RNA of some cells, usually it is mRNA that you sequence, that means that the sequence you are looking for is not an plain copy of the DNA gene sequence you have. Mainly because it results from splicing and other post-transcription processing. However, if you know the DNA sequence of the gene and you have RNA seq data (and if that particular gene was expressed in the cells the RNA is coming from), you can spot the exons of the gene in the data. If the gene is expressed in zebrafish you can find on ENSEMBL all the information about the transcripts of that gene and look for those in your RNA seq data (using BLAST for example) to confirm the presence of the expressed gene.

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