GgaINT0054916 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24945778-24946706:+
Coord C1 exon
chr5:24945778-24945946
Coord A exon
chr5:24945947-24946565
Coord C2 exon
chr5:24946566-24946706
Length
619 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
TTTCTTCCATTCTCTACCAGGAC
3' ss Score
11.12
Exon sequences
Seq C1 exon
ACTCCATGGATCCTATGAAGCTTTGAAAGGAGGCAACACCACAGAGGCCATGGAGGATTTCACTGGAGGGGTGACAGAGTTCTATGAGATAAAGGATGCTCCTAAAGATATCTATAAAATCATGAAACATGCCATTGCCAGAGGATCCCTCATGGCCAGCTCCATTGAT
Seq A exon
GTGAGTCCATATGAACTTTGTAGATGAGTCATAAGAAATGGCAGAAATCTCCACCTATAATCATGTACCAACTTTTGCAACAGCTTAGTTTAGTTCATGTAAGCAAACATTCATTTGCAGGTGGTAGGACACTCTCCTCTAGACACTTTCCATTAGAGAACAGCAAGCACCAAAAGGGAGATAGACAGAAGGAGAATAGGGAGGCAGGAGGAAGGAAGGGTGGGATCTGATCAGCAAAACCAGCACCCTGCTCTCAGTGAGGTGCAACAATTCTGTTAAGATACAAATCTTCATGTCAAAGATGCTAACAGTATGCAAATATCCAGGAAATTAACCTATTTGATCCCCAGCATATCCTTACATTATCTTAATTTAATGTGGTTAATTTAAAAAAGTGAAAGTAAGAAAACAAGTTTCGATAACAGTTGTGAAGTTGCAGTAAAAGCAGGAAAACAACTGGCAATACCAATCACCATAGATAACTGTGGACTATCTAGCATGTAAATAAGGAAGTAGAGAAGTTATCTAGGCCATTTTTCACCACTTATCTTTTTGTATAGTTTCTTTTCTATCCCCGTCTAATATTTCTGCACACCACTTTTCTTCCATTCTCTACCAG
Seq C2 exon
GACAACCTAGGCTTCTCCTACGGAGCAGCTCCTCGAAGTGACATTGGAGAACTGATTGCTCGAATGGTGAAGAACCTAGAAAATGCACAGATGACTTACTCCACTGTGGACTACCAGGGGACGGATGAAAGGCCAGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:5
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=0.021
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(16.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(13.4=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:
ACTCCATGGATCCTATGAAGCT
R:
CCAGGCTGGCCTTTCATCC
Band lengths:
310-929
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]