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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.

Input

  • Annotation of eight alternative transcripts from GENCODE Basic v24 (Download)
  • Chromosome 19 FASTA file from GRCh38/hg38 (Download)
  • Reference file (Download)
  • HMM file (Download)

 

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:

#chrgene_cluster_namename_hmmaccdescriptionbitscorestart_seqend_seqstart_genomicend_genomicfirst_sourcelast_sinkstart_modelend_modellength_modelsequencevariants
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin35.23096706011102-55147129-55134152-55147168-551471681134134ENST00000588426.5ENST00000588426.5
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin98.646547948985205-55141239-55134200-55147168-551471681134134ENST00000588981.5ENST00000588981.5
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin139.05754669871135-55141281-55134152-55147168-551471681134134ENST00000587465.6ENST00000587465.6
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin139.05754669871135-55141281-55134152-55147168-551471681134134ENST00000585321.6ENST00000585321.6
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin139.05754669871135-55141281-55134152-55147168-551471681134134ENST00000536926.5ENST00000536926.5
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin158.357640789469205-55141287-55134152-55147168-551471681134134ENST00000291901.12ENST00000291901.12
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin158.357640789458194-55141287-55134152-55147168-551471681134134ENST00000356783.9ENST00000356783.9
EHITchr19

ENST00000291901.12,ENST00000356783.9,ENST00000587465.6,

ENST00000587758.5,ENST00000585321.6,ENST00000588981.5,

ENST00000536926.5,ENST00000588426.5

TroponinPF00992.17Troponin158.357640789458194-55141287-55134152-55147168-551471681134134ENST00000587758.5ENST00000587758.5
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