GgaINT0054914 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24944151-24945507:+
Coord C1 exon
chr5:24944151-24944269
Coord A exon
chr5:24944270-24945373
Coord C2 exon
chr5:24945374-24945507
Length
1104 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTCTATTTGCCTTCATTCAGTTT
3' ss Score
7.85
Exon sequences
Seq C1 exon
GCGATTGCTGGTTCCTGGCTGCCATTGCTTGCCTGACACTGAATAAAAAACTGCTCTGCAGAGTCATACCTCATGACCAGTCCTTCATACAGAACTATGCTGGCATCTTTCACTTCCAG
Seq A exon
GTGAGTCCCTTCATCTAGCATTAAGGGGATGTAATTATATTCACCCAACAGCAAGCTCATCTCTTGGCACACTGTTCCCTTTCCTTCTTCCACCCTGTGAAAGCATGAGCAACAACAGGAAAGGAAGAAGGATTGAATTCCTTCACCCCAGGCTCTTCCAGCAAGGCAGTCATGGAAGGTAATTAGGGAACATTAACCCACCCATGAAGCATTTGCAGATGCATGGCCTGTGTGTGTCAGATAGCAACAGGTGCTTGGTCTTGCCTTCCTGCTCAGCTGCAGTACTACAGCCAGCACAGAGATACTGGTGGTTGGCAAGAGCATCTATTTTTAGGGCCACAAGCAGCTGGTCTCTGTCGAAAATAAGTCACTGAAGAACTGATTTTTCAGAAGAGATTAACTGCTGTTTGTCTTCCCCGTGGTTCTCTAAAAACATCTCCCTTAAGATGGATGTATTGCCCAGGTAAATTCAGCACAGCTGCCTCCCTTCCCATGACATCGCTTTTTGGCACATTATAAAGCAGGACACAGCCCTCTACTTATAGCTGTCCAGAATTCAGGTGGCTGGAGGAACACCAGGTAAATCTGAAGGAATACAGACTCTCTGCATCTGATCACAATGTAAGCCAGAGCACGGCTTCTTGCACAGCTGCATTTACGTATCCATCCCATCCCAGTAATCTCACACTGTGTGGAGGAATTGTTATTTACAACTTCAACCATAATCTAGCTCTGAAGGAAGAGCTGGAAACACCTGAAATTAAGAAAAGGGAAGAGGAAATAGAAGGCCAGCAGCAGGCACAGTGTGCAGTGCCATGGTGGAACAGTCACATGCAAAGAGTCAACTTGCTCAAAATCTCCCAGGCAGGACTCCTGGTAGTGTTGAAACTCAGAACCATCTAACCACTCCAAACCAGGACCTGCAGTTCCTGCCAGCATAAGTTTGGTTGCCATGGCTCAGCTCTGACCTCAGGAAACAGAAAAGGGGGAAGTTTTAACAGCTGTAGAACAGTTCAGTGTTTCTCCTCTGCTCAGTTTTCCAGCCAGGCTCCCCTTTCCCTGCACACAGTGAACCCAGATGTTTTTCTATTTGCCTTCATTCAG
Seq C2 exon
TTTTGGCGCTACGGAGACTGGGTGGATGTCATCATTGATGACTGCCTACCCACATACAACAACCAGCTGGTCTTCACCAAATCCTCCCAGCGCAATGAGTTCTGGAGTGCTCTCCTGGAAAAGGCCTATGCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:3
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(11.4=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(12.8=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:
CGATTGCTGGTTCCTGGCTG
R:
AGAGCACTCCAGAACTCATTGC
Band lengths:
231-1335
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]