GgaINT0054931 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24959516-24960188:+
Coord C1 exon
chr5:24959516-24959594
Coord A exon
chr5:24959595-24960071
Coord C2 exon
chr5:24960072-24960188
Length
477 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
CATTTCTGGTCCCCCTGCAGGGT
3' ss Score
10.14
Exon sequences
Seq C1 exon
AAAATCTTCAAGCATTACGATGCAGACCATTCAGGAACCATTAACAGCTATGAGATGCGCAATGCAGTCAAAGATGCAG
Seq A exon
GTAATTCCACTGGTGTCCAATGCCCAGCAGCCAAATAAGCCTTATTTTGGTTCATGTATCACAGGGTGAGATCAGGAATACAGCCCAGCCATTTAAGGAGGGACCTTCCCCCCCCCAGCAGAGTTCTTATATATCCAAACTGCAAGGCTTGTGTGTCTCACCATCTAAGCAGATCTTTGAACTTCTCAGTGAATAAAGCATGGCATCTCAGTCTCACAAATGATAAAAATCAAAAGAGCACTAAAGTCAGCACTCACACTTGCCCAGTTTTACCCTTTTAATTTGAACAGAGTTTGTGCAATGCTTGTGCAGCTGCATTAAGAGCACACGGGATGTGCATCAGGGAGCCCAGCTGCATGCAGGTTAACTTTTAACAACGCAGGCACCCACCAAAATTACCTACTTGCTCTCATTTAAGCGGTGGATTTTTTATTGTTGCATAAGGAGCAATCAAACTCATTTCTGGTCCCCCTGCAG
Seq C2 exon
GGTTTCGGCTGAACAACCAGCTCTACGACATCATCACGATGCGCTATGCTGACAAGAACATGAACATCGACTTTGACAGCTTCATCTGCTGCTTCGTGAGACTGGATGCTATGTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:21
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:
PF0003627=EF-hand_1=PD(86.2=92.6)
A:
NA
C2:
NO
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:
TTACGATGCAGACCATTCAGGA
R:
TGAACATAGCATCCAGTCTCACG
Band lengths:
182-659
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]