GgaINT0078820 @ galGal4
Intron Retention
Gene
ENSGALG00000009360 | CAPN2
Description
calpain-2 catalytic subunit precursor [Source:RefSeq peptide;Acc:NP_990411]
Coordinates
chr3:17040267-17040693:-
Coord C1 exon
chr3:17040457-17040693
Coord A exon
chr3:17040337-17040456
Coord C2 exon
chr3:17040267-17040336
Length
120 bp
Sequences
Splice sites
5' ss Seq
ACGGTAGGT
5' ss Score
10.15
3' ss Seq
CGGGCTCGTTTTGTTCCCAGGAG
3' ss Score
8.18
Exon sequences
Seq C1 exon
ATGGCGGGGATGGCGGCGGCGCTGGCGAAGGAGCGGGCGGCGGCGGCGGGCGCGGGGCGGCACGGGCAGGCCGTGCCCTACGTGGGGCAGGACTTCGGGGCGCTGCGGCGGGAGTGCCTGCAGGGAGGCCGCCTCTTCCACGACCCGTCCTTCCCCGCCGGCCCCGCCGCTCTCGGGTACCGGGAGCTGGGGCCCAACTCCTACAAAACGAAGGGCGTCGTCTGGTGTAGACCTACG
Seq A exon
GTAGGTGCCCGGCTCGGGGCGCCCGAGATGCGAGGTGCCCGGCCGGCTCCATCCCCGCCGTCGTCCCTCTCTTCGCTCCCTCCTTCTCCTCCCGTAACGCCGGGCTCGTTTTGTTCCCAG
Seq C2 exon
GAGCTGTGTTCCTGTCCGCGGTTCATCGCCGGCGGAGCCACGCGCACCGACATCTGCCAAGGAGCCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009360:ENSGALT00000015245:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PU(11.3=43.0)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(39.0=100)
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:
CCTACGTGGGGCAGGACTTC
R:
AGGGCTCCTTGGCAGATGTC
Band lengths:
229-349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]