GgaINT0088802 @ galGal4
Intron Retention
Gene
ENSGALG00000010186 | CAPN1
Description
Calpain-1 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P00789]
Coordinates
chr3:29685378-29685779:-
Coord C1 exon
chr3:29685619-29685779
Coord A exon
chr3:29685548-29685618
Coord C2 exon
chr3:29685378-29685547
Length
71 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
CCGTGTCTTCTTCCTCCCAGCCA
3' ss Score
7.97
Exon sequences
Seq C1 exon
GATGTCTTTCCGGGACTTCATGAGGGAGTTCTCCAGGCTGGAGATCTGCAACCTAACCCCCGATGCCCTCACCAAAGATGAGCTCAGCAGGTGGCACACACAGGTGTTCGAGGGCACATGGCGCCGAGGGAGCACTGCTGGGGGCTGCAGGAACAACCCAG
Seq A exon
GTACCTCCCGCATCTCCGCTCTTGGAGATGTGATGCAGCCAGGTGTATCATCCGTGTCTTCTTCCTCCCAG
Seq C2 exon
CCACATTCTGGATCAATCCCCAGTTTAAGATCAAGCTGCTGGAAGAGGATGATGACCCTGGGGATGACGAGGTGGCTTGCAGCTTCTTGGTGGCCCTGATGCAGAAGCACCGTAGGAGGGAGCGGCGAGTAGGGGGCGACATGCATACCATCGGCTTCGCTGTCTACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010186:ENSGALT00000016557:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.018
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.9=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:
ATCTGCAACCTAACCCCCGAT
R:
CCCCAGGGTCATCATCCTCTT
Band lengths:
181-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]