Searching protein domains on alternatively spliced regions of human gene TNNT1
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.
Command line
Obtaining reference transcript sequence
$> astalavista -t astafunk --tref --gtf tnnt1.gtf --genome ~/example/genome/ > reference_tx.fasta
Creating reference file
$> hmmsearch --domtblout reference_file ~/Databases/Pfam/Pfam-A.hmm reference_tx.fasta
Obtaing a reduced HMM file
$> grep -v "#" reference_file | awk '{print $5}' | sort | uniq > list-hmm-tnnt1
$> hmmfetch -f Pfam-A.hmm list-hmm-tnnt1 > database.hmm
or skip these commands and use directly the whole database Pfam-A.hmm as parameter for the option [--hmm]
Running AstaFunk
astalavista -t astafunk --genome ~/example/genome/ --gtf tnnt1.gtf --reference reference_file --hmm database.hmm
Output
AstaFunk identifies six complete alternative events between the eight alternative transcripts of the gene TNNT1 (in the paper we present, just for an example, only two events). See the standard output:
| # | chr | gene_cluster_name | name_hmm | acc | description | bitscore | start_seq | end_seq | start_genomic | end_genomic | first_source | last_sink | start_model | end_model | length_model | sequence | variants |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 35.2309670601 | 1 | 102 | -55147129 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000588426.5 | ENST00000588426.5 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 98.6465479489 | 85 | 205 | -55141239 | -55134200 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000588981.5 | ENST00000588981.5 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 139.0575466987 | 1 | 135 | -55141281 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000587465.6 | ENST00000587465.6 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 139.0575466987 | 1 | 135 | -55141281 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000585321.6 | ENST00000585321.6 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 139.0575466987 | 1 | 135 | -55141281 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000536926.5 | ENST00000536926.5 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 158.3576407894 | 69 | 205 | -55141287 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000291901.12 | ENST00000291901.12 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 158.3576407894 | 58 | 194 | -55141287 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000356783.9 | ENST00000356783.9 |
| EHIT | chr19 | ENST00000291901.12,ENST00000356783.9,ENST00000587465.6, ENST00000587758.5,ENST00000585321.6,ENST00000588981.5, ENST00000536926.5,ENST00000588426.5 | Troponin | PF00992.17 | Troponin | 158.3576407894 | 58 | 194 | -55141287 | -55134152 | -55147168 | -55147168 | 1 | 134 | 134 | ENST00000587758.5 | ENST00000587758.5 |
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