GgaINT0054923 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24952878-24953827:+
Coord C1 exon
chr5:24952878-24953086
Coord A exon
chr5:24953087-24953790
Coord C2 exon
chr5:24953791-24953827
Length
704 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TTATTTCTGCTTTCTTCTAGGGA
3' ss Score
11.15
Exon sequences
Seq C1 exon
ATGCACGGTACTAAGCACCACTTGCAAAAGGATTTTTTCCTCTACAATGCTTCCAAAGCTAGAAGTAAGACCTATATAAACATGCGAGAAATCTCTGAGCGCTTCCGGCTGCCTCCCAGCGAGTACGTTATCATCCCATCCACATACGAACCCCACCAGGAGGGAGAATTCATCCTGAGGGTTTTCTCAGAGAAAAGAAGTCTTTCAGA
Seq A exon
GTAAGTTGCAGATCTTTCATCTGGCTCTAAAGGAGGAACTGAGCTCACTACTCTGTTATAGTTGTGTTCCCTGCTTGCAACACTCTACTCCCAGTTTTCTTAATCCCATTAGAAACTCCAAGATGCGAACACATATCCCCAGTATTACCTTGTAGTTTAACAAAAACCTGCTTTGGATTTCTATTGGAGACTCTGGAGACTACTGGCAGGATATCCTTTGTGAACATGCTTTCTGCTCTTTTTATAATGAAAACCAACAAGTTTGTTATGCAATGCTATATGCCACCGCTATATCCCATATGGAAGTTTTTGCCAGATAGATCACTGAGACACATCTAATTTCAGTCATGAACAAAATCCAGAAATAGGTGTTATTTCTTTTCCATCCTGCTCTTTAAGTAGCTTCCCAGACCTCAAACTGCAGCTAGTATCACCTTGCTTAGGCCAAAAAACTTCTGGTTTGCTCCCAGCAGTCAAGGTTCAGTGATGCCAAGGTATCACGTAAGGGAAATAAACCAGGCAGCAGTGTTCTTGGAAGCAGTACTTGGGATGCTCAGCTCAAACTCAGAAAAACTACATCCAGAGTCTGAGCTGTAGTGCCTGGAAGCCAGCCCACACACTGCCTACTTACAAAGCACATGCAGAAACAAGCAGTGTTGGAAACAGACACCTTCCTGATTTATTTTATTTCTGCTTTCTTCTAG
Seq C2 exon
GGAGGTTGAAAACATGATTGAGGCAGATCGCCCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.769
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(44.5=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:
ATGCACGGTACTAAGCACCAC
R:
GCGATCTGCCTCAATCATGTT
Band lengths:
240-944
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]