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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.
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$> astalavista -t astafunk --tref --gtf tnnt1.gtf --genome ~/example/genome/ > reference_tx.fasta |
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$> hmmsearch --domtblout reference_file ~/Databases/Pfam/Pfam-A.hmm reference_tx.fasta |
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or skip these commands and use directly the whole database Pfam-A.hmm as parameter for the option [–hmm]. |
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astalavista -t astafunk --all --genome ~/example/genome/ --gtf tnnt1.gtf --reference reference_file --hmm database.hmm |
chr | gene_cluster | variant | acc | bitscore | start_seq | end_seq | start_genomic | end_genomic | first_source | last_sink | start_model | end_model | length_model |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000588426.5 | PF00992.17 | 35.2309670601 | 1 | 102 | -55147129 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000588981.5 | PF00992.17 | 98.6465479489 | 85 | 205 | -55141239 | -55134200 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000587465.6 | PF00992.17 | 139.0575466987 | 1 | 135 | -55141281 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000585321.6 | PF00992.17 | 139.0575466987 | 1 | 135 | -55141281 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000536926.5 | PF00992.17 | 139.0575466987 | 1 | 135 | -55141281 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000291901.12 | PF00992.17 | 158.3576407894 | 69 | 205 | -55141287 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000356783.9 | PF00992.17 | 158.3576407894 | 58 | 194 | -55141287 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,ENST00000536926.5,ENST00000588426.5 | ENST00000587758.5 | PF00992.17 | 158.3576407894 | 58 | 194 | -55141287 | -55134152 | -55140883 | -55149354 | 1 | 134 | 134 |
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Description of the output columns can be found in 3.4 - Tool ASTAFUNK (Prediction of functional domains impacted by AS).