According to RefSeq (NM_003283),
This gene encodes a protein that is a subunit of troponin, which is a regulatory complex located on the thin filament of the sarcomere. This complex regulates striated muscle contraction in response to fluctuations in intracellular calcium concentration.
$> astalavista -t astafunk --tref --gtf tnnt1.gtf --genome ~/example/genome/ > reference_tx.fasta |
$> hmmsearch --domtblout reference_file ~/Databases/Pfam/Pfam-A.hmm reference_tx.fasta |
or skip these commands and use directly the whole database Pfam-A.hmm as parameter for the option [–hmm]. |
astalavista -t astafunk --genome ~/example/genome/ --gtf tnnt1.gtf --reference reference_file --hmm database.hmm |
Description of the output columns can be found in 3.4 - Tool ASTAFUNK (Prediction of functional domains impacted by AS).
Look the results in the UCSC Genome Browser. Convert our output to BED track:
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