DreINT0005719 @ danRer10
Intron Retention
Gene
ENSDARG00000045199 | CAPN1 (1 of 2)
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:HGNC:1476]
Coordinates
chr7:6567228-6568035:-
Coord C1 exon
chr7:6567875-6568035
Coord A exon
chr7:6567389-6567874
Coord C2 exon
chr7:6567228-6567388
Length
486 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCA
5' ss Score
7.33
3' ss Seq
AAAATCTTTTCTTCCCACAGCAA
3' ss Score
8.96
Exon sequences
Seq C1 exon
GATGTCGTTCAGTGATTTTCTGCGCGAGTTCACCCGTTTGGAAATCTGTAACCTGACGGCGGACGCTCTCCAGGCCAGTCAGGTGAAGAAGTGGAGCACCGCCAACTATAACGGCGAGTGGAGGAGAGGAAGCACTGCAGGTGGCTGCAGGAACTATCCAG
Seq A exon
GTATCAGATTTAATTAATAATAATAATAATAATAATTCCTTACATTTATATAGTGCTTTTCTGGGCACTGAAAGCACTTTACACAATGGGGGGGGGATCTCCTCATCCACCACCAGTGTGCAGCATCCACCTGGATGACGCGATAGCAGCCATTTTGCGCCAGACCGCACACCACACACCAGCTGATTGGTGGAGAGGAGACAGTGTGATGAAGCCAGTTATGATATGGGGAGGGTTAGGAGGCCATGATGGACAGAGGCCAGTGGGCAGATTTGGCCAGGATGCCGGGGTTAAACCCCTACTCTTTTTCGAAGGACATCCTGGGATTTTTAACGACCAAAGAGAGTCGGGACCTCGGTTTAACAACTCATCCGAAAGATTGTGTTGTTGCCGAAGTTTTCCCTACGCTATGGACGCTTTTCACATTCACGAGTTTCACAGTAGCAGAAGTCATCATAGTTGGTTCAAAATCTTTTCTTCCCACAG
Seq C2 exon
CAACATTCTGGATCAACCCGCAGTTCAAGGTGGCCCTGAAACACCCGGATTCTCCCGGCCAATCAGAGTGCAGCTTCCTGGTGGCGCTGATGCAGAAGGACCGCAGGAAGAAGAGAAGAGAAGGGCAGGACATGGAGACTATCGGATTCGCCATTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045199:ENSDART00000113658:10
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=0.071
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.8=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(34.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCGTTCAGTGATTTTCTGCGC
R:
TCATAAATGGCGAATCCGATAGTCT
Band lengths:
318-804
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]