GgaINT0088811 @ galGal4
Intron Retention
Gene
ENSGALG00000010186 | CAPN1
Description
Calpain-1 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P00789]
Coordinates
chr3:29682031-29682668:-
Coord C1 exon
chr3:29682590-29682668
Coord A exon
chr3:29682148-29682589
Coord C2 exon
chr3:29682031-29682147
Length
442 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
GAGTACTCCCTGCCTTTCAGGTT
3' ss Score
8.09
Exon sequences
Seq C1 exon
ACAATCTTCCGCCAGTATGACCTGGATAAATCAGGCACCATGAGCTCATACGAGATGCGCATGGCTCTAGAGTCAGCTG
Seq A exon
GTAAGTCTGGAGAGGATGGGGCTGGGCTGAGGGTGGAGGAACACTGTAGGAGCTCTGTCTCAAGTAGCTGGAGAACCGTGGAACCAGCCTACATTGTGAGCTTTGAGCCAATCTGTCATGAGATGAGGCCTATATGTAAGCTGGATTCTCTCCCACCAATCCTCGCTTGTTGCTGGCATCCTCAGAGCCGGGATACACACAAGGTTGTCCCAGCCATCCTCATCTGACCTGTGAGGTCCCATCCTGGCAAAGTCGGGTCAGTGAGCTAGCATTCATTTGGCAATGGGCTGTAGCTCCAGGAAGAGCATCCCTTACTCCTACCAAAGCTAGGTTCAATGGCCTTCCTTGGGTGGGGTGTTGGCCCCTTCTGGTGAGAACATGAACTTTGATAGTTGCATTTTCTCCCACCTCTTGTGGGTGCTGAGTACTCCCTGCCTTTCAG
Seq C2 exon
GTTTCAAGCTGAATAACAAGCTGCATCAGGTGGTGGTTGCCCGTTACGCAGATGCTGAGACGGGCGTGGACTTCGACAACTTTGTCTGCTGCCTGGTGAAGCTGGAGACAATGTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010186:ENSGALT00000016557:18
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:
PF0003627=EF-hand_1=PD(89.3=92.6)
A:
NA
C2:
NO
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:
ACAATCTTCCGCCAGTATGACC
R:
ATTGTCTCCAGCTTCACCAGG
Band lengths:
191-633
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]