GgaINT0096413 @ galGal4
Intron Retention
Gene
ENSGALG00000012617 | ChALK5
Description
TGF-beta receptor type-1 precursor [Source:RefSeq peptide;Acc:NP_989577]
Coordinates
chr2:56039576-56040641:+
Coord C1 exon
chr2:56039576-56039827
Coord A exon
chr2:56039828-56040398
Coord C2 exon
chr2:56040399-56040641
Length
571 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
ACTGTCTTGTTCACCATCAGGTC
3' ss Score
9.63
Exon sequences
Seq C1 exon
CATTACAATGTTACTGCCATCTATGCACAAAGGACAACTTTACCTGTGTGACAGATGGGCTTTGTTTTACCTCTGTAACACGGACTGCAGATAGAGTCATACGCAATAGCATGTGTATAGCAGAAATTGATCTGATTCCTCGAGACAGGCCATTTATTTGTGCACCATCCTTCAGAGATGGAGTTACTACTTTGCCTCATTGCTGTGACAGAGACCACTGCAATAAAATAGAACTTCCAATTCCAACACCAG
Seq A exon
GTAATAGTTTTTGATGTATTTGTTTTCTAATCTATTTTTAACAATGGAAAATTCTGAAAGAATTCTAGTTTTGAAGTTGCTGATGAACTTGAGGGTCTGAACTATACCTTAGATTCTGCATATAAAATTTCGAGAGTTTTGGAATAAGACATTTCTATTCTGGGTAGGAACGGTAGGGCTAGTTTCACAGCTTCTGTGCAAGGTAAATATAAACTGAATATGCAAGACGATCAGGCACTGGAACAGGCTCACTCACAGTGCAGTAGTCTCAACACCAAGCAAGCTGAAATTCACTAAGTGTTTGGACAATGCTTTCGCATGTAGGGTTTCAATTTTGGGTGGTCATGTGTAGGAGCCATGAGTTGGGCTTGAAGATCCTTGTGGATCCCTTCCAATTCTGGGTATTCTTTGAAATAGTTACTTTTGTCTCCTGTAATACTTTTTTTGTGCAATAACTTTTTGAAGAATGGTTCTTAAGAAATGTAATTCAAATACCATTAAGTAAATAAACTTCATGTATTTCATGATGTTACATAGAAGGAAATGGTAAAACTGTCTTGTTCACCATCAG
Seq C2 exon
GTCCTACTCCAGGAAGACCAGCTTCTAGTCTAGGACCTGTGGAACTGGCAGCTGTTATTGCTGGACCTGTCTGCTTTGTCTGCATTTCATTGATGCTGATTCTGTATCTTTGTCATAACCGTACTGTAATTCATCATCGTGTGCCAAGTGAAGAAGATCCTTCATTGGATCGTCCCTTTATATCTGAAGGAACTACTTTGAAGGATTTAATTTATGATATGACAACTTCAGGCTCTGGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012617:ENSGALT00000020598:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.035 A=NA C2=0.159
Domain overlap (PFAM):
C1:
PF0106418=Activin_recp=WD(100=95.3)
A:
NA
C2:
PF085157=TGF_beta_GS=PU(58.6=20.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTCTGTAACACGGACTGCA
R:
ATCTTCTTCACTTGGCACACGA
Band lengths:
342-913
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]