GgaINT0110207 @ galGal4
Intron Retention
Gene
ENSGALG00000000750 | CAPN5
Description
calpain 5 [Source:HGNC Symbol;Acc:HGNC:1482]
Coordinates
chr1:192462877-192463661:-
Coord C1 exon
chr1:192463539-192463661
Coord A exon
chr1:192463074-192463538
Coord C2 exon
chr1:192462877-192463073
Length
465 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
CCTCTGTGCTTTCTCCCCAGGTG
3' ss Score
13.45
Exon sequences
Seq C1 exon
TATGTATTTGATGTGAAGAAGGCAGAAGATGAAGTGCTGATCTCCATTCAACAGAAGCCAAAAAGGACCAGTCGCAAAGAAGGCAAAGGAGAGAACTTAGCCATAGGCTTTGATATCCACAAG
Seq A exon
GTAAACTGTGGGTCCTGCATGCTAGCCTGCATGCCCTCAGTAAATTACTAGTACTGCATGACCATTGACATGATGTGTTTAGTCATCACTCTGTGTGCCCCATGGGTGCCTTCAGCACATCCTGCAGTGATGGTGGGAGATTTCAGAAATGAATAGGGTCAGCACAGACTTGCTTTCCTTGCTGAAAGCAGTGGATTGTCTGTCACCTCTGAATTTCACAAGATTGATCAAGTGTTTCTTGGTGGTCCCCCAGTGTCAAGCTGGAATGCAACTCAGAATGAGTTTATGAGCCAAGTGAGTTTTGAGAGGCACCTCAAATTTCATTTGGGACCACTTTGCTGGTTCTCTTAATTCTGGCTGTCCCATCACTGTGGAATCAATTCTTGCTGGCTGTCCCCTAACCTGGTAACTGATACATTTCCTCAGTGCTGTCCTGCTGACTGTCCCTCTGTGCTTTCTCCCCAG
Seq C2 exon
GTGGAGCTGAACAGGAACTACCGGATGCACACCCTGCAGCAGAAGGTGGCCAGTTCCATTTACATCAACTCCCGTAGTGTCTTCCTGAGGACGGACCTGAAGGAAGGTCGCTATGTCATCATCCCCACCACTTTTGACCCTGGTCATGTAGGCGAGTTTCTTCTCAGGATTTTCACAGATGTGCCTTCGGATTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000750:ENSGALT00000001093:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.244 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(27.8=100)
A:
NA
C2:
PF0106717=Calpain_III=FE(45.1=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:
TGTATTTGATGTGAAGAAGGCAGA
R:
CCGAAGGCACATCTGTGAAAA
Band lengths:
311-776
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]