In a well annotated GTF/GFF file, The genomic coordinates of exons of genes are present. A gene can produce different isoforms by a mechanism known as alternative splicing. If we try make different permutation/combinations to join the exons of a gene in-silico, we can get different isoforms of a gene. Suppose we get 14 isoforms of one gene. Out of 14, 9 isoforms/transcripts are reported in ensembl/NCBI-genpept or other protein seq repository while 5 are not reported till date. so are they 5 transcripts/isoforms are novel which are being come out from known exon junctions of available GTF/GFF file?
In RNA-seq novel junction finding strategies, we came across with some novel junction (new splice sites in known exons) coordinates which are not specified in the GFF/GTF file. Some isoforms may be generated by splicing from these novel junctions. so my question is that are these transcripts will be considered novel or the above mentioned 5 transcripts or both?