GgaINT0078827 @ galGal4
Intron Retention
Gene
ENSGALG00000009360 | CAPN2
Description
calpain-2 catalytic subunit precursor [Source:RefSeq peptide;Acc:NP_990411]
Coordinates
chr3:17030161-17030569:-
Coord C1 exon
chr3:17030495-17030569
Coord A exon
chr3:17030322-17030494
Coord C2 exon
chr3:17030161-17030321
Length
173 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGC
5' ss Score
8.72
3' ss Seq
GTTGGCATTGCCTCCCCCAGGAT
3' ss Score
6.64
Exon sequences
Seq C1 exon
CTGCCCAAACTGGAGTGGTGTTGACCCAGAGGTGCGGGAGCGGCTGACGAGGAGACATGAGGATGGGGAGTTTTG
Seq A exon
GTAAGCAAATGAGCCTTTTTCCCACACAAAGTACCCTCTCCCACCACACTCTCCAAGACGAGTGAGCAAATTCACCCCAAATCCCAGTGCTAAGTTGCTGCAGTAGAGGGAGTAGGTAGACAAGGTGGCTGGAAACACCGTCCATCTTAAAGAGTTGGCATTGCCTCCCCCAG
Seq C2 exon
GATGGCCTTCAATGACTTCCTGAGGCACTACTCCCGCCTGGAAATCTGCAATCTGACTCCAGACACTCTGGCAAGTGACAGGTACAAGAAGTGGAGCCTGCTGAAGCTGGATGGGAACTGGCGGCGAGGAGCTACTGCGGGGGGCTGCAGGAATTACCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009360:ENSGALT00000015245:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
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:
GCCCAAACTGGAGTGGTGTTG
R:
TTGGGTAATTCCTGCAGCCC
Band lengths:
234-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]