GgaINT0054915 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24945374-24945946:+
Coord C1 exon
chr5:24945374-24945507
Coord A exon
chr5:24945508-24945777
Coord C2 exon
chr5:24945778-24945946
Length
270 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTTTTTTCCTCTTTCCAAGACT
3' ss Score
7.05
Exon sequences
Seq C1 exon
TTTTGGCGCTACGGAGACTGGGTGGATGTCATCATTGATGACTGCCTACCCACATACAACAACCAGCTGGTCTTCACCAAATCCTCCCAGCGCAATGAGTTCTGGAGTGCTCTCCTGGAAAAGGCCTATGCAAA
Seq A exon
GTAAGTCAACCTGCTGCACCGTGTCATGCTCTCTTTGGCTGGGGTGGGGGGGTAGATGAACTGCTTTGTACTGACCTTGTCATATGCACTTTAGCTCTACACACATCAGTGCATTTTTCCACAGATTCTACGTGAGTATGTCGTAAAGCATATTTTCTAGGGTTGCTCTTTTGGAGGGTGTTTTTGTTGCTCATTCAGAAGCCTATATTTGATTCTCAGCATCTTTTTCTTTGGTTTTTCTTTTTGTTGTTCTTTTTTCCTCTTTCCAAG
Seq C2 exon
ACTCCATGGATCCTATGAAGCTTTGAAAGGAGGCAACACCACAGAGGCCATGGAGGATTTCACTGGAGGGGTGACAGAGTTCTATGAGATAAAGGATGCTCCTAAAGATATCTATAAAATCATGAAACATGCCATTGCCAGAGGATCCCTCATGGCCAGCTCCATTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:4
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=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(12.8=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(16.3=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:
TTTTGGCGCTACGGAGACTG
R:
GAGCTGGCCATGAGGGATCC
Band lengths:
296-566
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]