DreINT0005757 @ danRer10
Intron Retention
Gene
ENSDARG00000055338 | CAPN1 (2 of 2)
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:HGNC:1476]
Coordinates
chr21:27454595-27454997:-
Coord C1 exon
chr21:27454837-27454997
Coord A exon
chr21:27454756-27454836
Coord C2 exon
chr21:27454595-27454755
Length
81 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
GACTGATTCTCTCAACACAGCAA
3' ss Score
3.91
Exon sequences
Seq C1 exon
GATGGCGTTCAGTGACTTCAAGCGAGAGTTCAGCAGACTGGAGATCTGTAACCTGACAGCGGATGCGCTCCAGAGCCGAGAGGTGAAAAAGTGGAACTCGTCGCTGTATCCTGGTGAATGGAGAAGAGGATCCACTGCTGGCGGATGCAGGAATTATCCAG
Seq A exon
GTACCTTCTCCACCAGAGTCTCTTTATTGCTTTTAAGCTGAGACAGCGCTCTTGAATTAAAGACTGATTCTCTCAACACAG
Seq C2 exon
CAACATTTTGGATCAATCCCCAGTTTAAAATAGTGCTGAAGGAACCAGATACTGACAATCAAGAAGGCTGCACTTTTCTAGTGGCTCTGATGCAGAAGAATCGCAGACAGTTACGGAGGGAGGGCAAAGACATGGAGACCATTGGATTTGCCATTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055338:ENSDART00000077657:9
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=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.7=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(34.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGCGGATGCAGGAATTAT
R:
ATGGTCTCCATGTCTTTGCCC
Band lengths:
167-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]