GgaINT0088797 @ galGal4
Intron Retention
Gene
ENSGALG00000010186 | CAPN1
Description
Calpain-1 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P00789]
Coordinates
chr3:29688131-29688540:-
Coord C1 exon
chr3:29688407-29688540
Coord A exon
chr3:29688300-29688406
Coord C2 exon
chr3:29688131-29688299
Length
107 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TCTCACTGCCCGGTGCTCAGGCT
3' ss Score
4.55
Exon sequences
Seq C1 exon
ATCTGGCAGTTTGGTGAGTGGGTGGACGTGGTGGTGGACGACCTGCTGCCCACCAAGGACGGGGAGCTCCTGTTTGTGCATTCAGCAGAGTGCACAGAGTTCTGGAGTGCTCTGCTGGAGAAGGCTTACGCCAA
Seq A exon
GTGAGTCCGACCACTGCGGGCACAAAGTTGCAGGGGGGGGTGGGGCGGAGCAGCAGCACAGTGTGCCCTCATCACCTCACGTGCCTCTCTCACTGCCCGGTGCTCAG
Seq C2 exon
GCTGAACGGCTGCTACGAGTCGCTCTCAGGGGGCAGCACCACTGAGGGCTTTGAGGATTTCACCGGCGGCGTAGCGGAGATGTATGACCTCAAGCGGGCACCGCGCAACATGGGCCACATCATCCGCAAGGCACTGGAGAGGGGGTCCCTGCTGGGCTGCTCCATCGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010186:ENSGALT00000016557:4
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(14.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.7=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:
CAGTTTGGTGAGTGGGTGGAC
R:
CGGATGATGTGGCCCATGTTG
Band lengths:
254-361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]