GgaINT0088805 @ galGal4
Intron Retention
Gene
ENSGALG00000010186 | CAPN1
Description
Calpain-1 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P00789]
Coordinates
chr3:29684371-29684784:-
Coord C1 exon
chr3:29684573-29684784
Coord A exon
chr3:29684411-29684572
Coord C2 exon
chr3:29684371-29684410
Length
162 bp
Sequences
Splice sites
5' ss Seq
AGCGTGAGT
5' ss Score
8.2
3' ss Seq
CCTCCTCTTTCTGCCCCCAGGGA
3' ss Score
13
Exon sequences
Seq C1 exon
GCCCAGGGAAGCCAGAATGTGCACTTGAAGAAGGACTTCTTCCTGCGAAACCAGTCGCGGGCACGCTCTGAGACCTTCATCAACTTGAGGGAAGTGAGCAACCAGATCCGGCTGCCCCCTGGCGAGTACATCGTTGTGCCCTCCACCTTTGAGCCACACAAGGAGGCCGACTTCATACTGCGGGTCTTCACCGAGAAGCAGTCAGACACAGC
Seq A exon
GTGAGTCTTCACCACAAAGCCTTCTGCCACGTCCCAGCCCCTTGCCTTGTTAGGGAATGTGTTGGCCCAGGTCATCACATGTGTTGGTGAGTGCTGCAGCAGATTCCACTGACCTCCCGTCACTGTGTGCACCCCCCCCCCCCCTCCTCTTTCTGCCCCCAG
Seq C2 exon
GGAGCTGGATGAGGAGATCTCGGCAGACCTGGCAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010186:ENSGALT00000016557:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.595
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(44.9=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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAGGGAAGCCAGAATGTG
R:
CAGGTCTGCCGAGATCTCCTC
Band lengths:
242-404
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]