GgaINT0087012 @ galGal4
Intron Retention
Gene
ENSGALG00000011136 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:HGNC:1486]
Coordinates
chr3:39832195-39833211:+
Coord C1 exon
chr3:39832195-39832403
Coord A exon
chr3:39832404-39833174
Coord C2 exon
chr3:39833175-39833211
Length
771 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
TAAGGTTTTGTTTTCCCCAGGGA
3' ss Score
8.7
Exon sequences
Seq C1 exon
AGCCCTGGTGGAGATGAACACTTGAGCAAAGACTTCTTCAGGTACCACGCCTCCAAGGCCAGGAGCAAAACCTACATCAATTTAAGGGAAGTGTCTGACAGATTCAAGCTGCCACCAGGTGACTACATCCTCATTCCAACCACATTTGAGCCACATCAGGAGGCAGATTTCTGCCTGAGAATCTTTTCAGAGAAGAAGGCCATCACTGA
Seq A exon
GTAAGTCAGCAGAAAGCACCAGGCCTTTTGGTGCTTTCCTCTGCATGGGGCTGCCAACTCCTGGGAAGGGTCTGGATGCTGGGTGCCCGGTCCTATGACAGAACCCTGTTGTGGGAAGCTCCTGAGGGCTTTTTGCCACTTTGCAATTTTTATTTGCTTAGTAAGGAGAATAAGGAAAGGTCTGAAAAAGGGTATTTGGCCTGCAGCATGCCCTCCAATGTGAGGCTGAGCTAGGTCAAGGCTCATCTGCCTGGTTCCTTTCAAAGTGGTCAGGAAAAATCCATCTGCAGATGCATTTGCCCATTTCTGCTAAATCTGGCTATTTTGGAGAGCAGTGTAAGAGGTGGAGACATATGGCTTGCCATGGTGAATCCAATGGAAAAACTGCTAGCTGCCTGCTGCTGTTCAGTAATATGTTTGGTTCCTCTTTGTTTCCTCACAAAGTATGCCCACATGACAATTCTGTATGAAAAAAAAAAACCTGAGGGAAAAAGTGCACAATTAATAAGATTAATTCTTTTGCAGACAGCATGCACGGAGGCTATGCCCTCACTGAGTCCTGCTTAAAATCTGTTATAACGGCTCATGCCAAAATTTGAACTGTGCAAAAATCTCTCTGATTAATTTTGTCTAAACATAAGTAGTTCAGTAAGAAAAAAATGCAGTTTTATCTTTCACCTCTGGAAAATGTAATGAGCAAGCTTGTGCCCTTTCCACCCCAAGCAGACACTGAACATCTTCAGATACTGAATAAGGTTTTGTTTTCCCCAG
Seq C2 exon
GGATCTGGATGAAAATGTTGCCATTGATCTCCCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011136:ENSGALT00000018152:11
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=0.538
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(46.9=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:
AGCCCTGGTGGAGATGAACAC
R:
CTCGGGGAGATCAATGGCAAC
Band lengths:
246-1017
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]