BtaINT0031236 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010230 | CAPN1
Description
Bos taurus calpain 1, (mu/I) large subunit (CAPN1), mRNA. [Source:RefSeq mRNA;Acc:NM_174259]
Coordinates
chr29:44085314-44085665:+
Coord C1 exon
chr29:44085314-44085525
Coord A exon
chr29:44085526-44085625
Coord C2 exon
chr29:44085626-44085665
Length
100 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TCTCTCCCCACCCTCTGCAGAGA
3' ss Score
9.68
Exon sequences
Seq C1 exon
CTGATGGGCCAGCCGGCCGTGCATCTGAAGCGGGACTTCTTCCTGTCCAACGCCTCCCGGGCCCGGTCCGAGCAGTTCATCAACCTGCGGGAGGTCAGCACCCGCTTCCGCCTGCCGCCTGGGGAGTACGTGGTGGTGCCCTCCACCTTCGAGCCCAACAAGGAAGGTGACTTTGTGCTGCGTTTCTTCTCAGAGAAGAGCGCAGGGACCCA
Seq A exon
GTGAGTAGAAAGCCCTCCCCTGTCTCCCCCTTTCCTCCCACCACACCCTTGCTGCCCCAACCCCCGTTGACTGGCCCCTCTCTCTCCCCACCCTCTGCAG
Seq C2 exon
AGAGCTGGATGACCAGGTCCAGGCCAATCTCCCCGACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010230:ENSBTAT00000011678:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.571
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(43.8=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCATCTGAAGCGGGACTT
R:
CTCGTCGGGGAGATTGGCC
Band lengths:
234-334
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]