GgaINT0088794 @ galGal4
Intron Retention
Gene
ENSGALG00000010186 | CAPN1
Description
Calpain-1 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P00789]
Coordinates
chr3:29689955-29690820:-
Coord C1 exon
chr3:29690538-29690820
Coord A exon
chr3:29690025-29690537
Coord C2 exon
chr3:29689955-29690024
Length
513 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
TCAATACTCTCCTTATGCAGGAA
3' ss Score
8.64
Exon sequences
Seq C1 exon
GACACAGAGGTGGAGGTAGCGGTGCCAGTACGCAGCTATGATGCCCTTTGGGGGGATCGCTGCCCGGCTGCAGAGGGACCGCCTGAGAGCCGAGGGGGTCGGCGAGCACAACAACGCTGTCAAGTACCTCAACCAGGACTATGAAGCCCTCAAGCAAGAGTGCATCGAGAGTGGCACCCTCTTCAGGGACCCCCAGTTCCCAGCTGGCCCCACTGCCCTCGGCTTCAAGGAGCTGGGGCCATACTCCAGCAAGACACGGGGCGTGGAGTGGAAGCGTCCATCG
Seq A exon
GTAAGTGCTGGGCTCATGTCCTTCGCCTGCAGTTTCTGCATTAATGTGGTGTGCCAAGCTGCAGCCTGGCTTCAATTTGCTTCTTACTGTGCTTAAAGTTCCTCACGTGCTTCATTGCCCATTCCCCAGAGGAATACTGCTCGCTGAGTACTCAAAGAGCATTGTGTCTAGCACACCCTTCATCCTCTAGGCAGTATACATTGGCCTTTACAATGGGAGAGTTGTGCCATTGCTTCTGGATGTCCCAGCATAGGTGTGACACCCTCGGTGACTCTTGGGGTTGTGTATCCATTGGTGCCACGAGTTCAGGGGCAATGCCCATCTAGCCATTTCCTGCTGAAGAAGATCTTGCCTTGCCTTCCTATGATGGCCTTAATGTTGCACTCAAGCGGTTTTCCCAGGCAGAGGGCAGGTGGGGTGCATCTCGGAGATGATAATCCCATTCTCCCGAGTCAGTGCTACAATGGGCACAGGTCCTGCTGAGATCCAATGCTCAATACTCTCCTTATGCAG
Seq C2 exon
GAATTAGTGGATGACCCTCAGTTCATCGTTGGTGGTGCAACCCGGACAGATATCTGCCAAGGAGCTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010186:ENSGALT00000016557:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PU(11.3=41.5)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(7.7=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:
CAGAGGTGGAGGTAGCGGTG
R:
CCAGAGCTCCTTGGCAGATAT
Band lengths:
349-862
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]