Did you try from here Gencode or trytripdb

https://www.gencodegenes.org

https://tritrypdb.org/tritrypdb/app/record/dataset/DS_8bc463a882

https://www.crg.eu/en/programmes-groups/guigo-lab/datasets/u12db-database-orthologous-u12-type-spliceosomal-introns

if not then try to get sl sites homologous to your organisms and create a local database.

Then RNA-seq pipeline to extract SL sites of your organisms manually from RNA-seq data.

Retrieve your RNA-seq reads of your organism align your reads with corresponding reference genome using tophat or hisat-2.

try to pick consensus fastq from alignment using samtools and filter by bedtools.

Then convert it into fasta and try blast+ against your locally created sl homologus database.

Anuraj Nayarisseri Anuraj, To get consensus fastq and fasta, I have used following command. samtools mpileup -uf genome.fasta rna.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fastq seqtk seq -aQ64 -q20 -n N cns.fastq > cns.fasta

However, Could you please correct me if I am wrong, The consensus fasta sequence contains consensus region between the genome and RNA-seq. And those regions of genome are expressed. Thanks you