MmuINT0028648 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:5988545-5990050:-
Coord C1 exon
chr19:5989992-5990050
Coord A exon
chr19:5989388-5989991
Coord C2 exon
chr19:5988545-5989387
Length
604 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTGTCTGTCTTGCCCTGCAGTGG
3' ss Score
10.85
Exon sequences
Seq C1 exon
GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTTAAG
Seq A exon
GTGAGATAATCCCCCCTGTTCACCCAACCCGACCAGGACAGGCGTCCACGGCCTTGGAACAAGGCTTCAAATCTGGACCCCAGTCTTGGAAGCTTCTGAAGCCTGGGGGGTGGGGGATGAAGAAGGGGAGGCCAGGCTTCTAGAAGCTGGTGGGAACCAGCAGCCTAACGTTCCAGAGTAGAGAAATGAGACAGCTGCTGCTGACTGTGGCGGTGACTCAGGCCCAACCCGAGGGAGGCAGAGACAGGTGGAGTTCTGGGAGTTTGAGGCTAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCATGGACTGTCCTTGTCTCAAAAAAAAACAGAGAAAAGCCAAACATACACACATACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAAGAAGAGGAGGAGGAGGAGGAGGAGAAGAAGGAGAAGCGAACACCCCTGTTGAGGGCATAAATATTATAAATATTGCTTGGTGATGGCTGAGCCCAGTCTGCAGTCTGTCCTCTGGGATGGGTGATGGGTAAAGGAAGAAGCTGACTGGCCATGTGTCCTGCAGCTCCAAGTAACCTGTCTGTCTTGCCCTGCAG
Seq C2 exon
TGGCTCCAGCTGACTATGTTTGCCTGAAGTGGGGAATCGCTCCGCTCCAGTTGCCTTTGTTCTTCCATTCTTCCTCTGCCAAGCCACGCCTCCCCGCCAAGCCACGCCTCCCCGCCGTGCCACTCCAGACTACACCAGCTTCTGGTGCCTTCCTCAGAACAGGAAGGAAGGCACCCTTGTCCTCCTGTTCCCCTTGTCCTCCTGTCCTTTCACCTCCCCACTACCTCTGTTCGACTGCTCTGGGCAGTCACGGGGCCCTCCCTGCCCCTGTAGTCAGACTGGGCACCCTGACCCCTGCTCAGGGCTAAGACCAGGAAGACAGCTCCCTGCTCATCCCTGCCTCGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGCACCCCTGCCTCCCCCTCGCTGCTACTGTCCGGATGTGAGTCTTGCCTAATCTGTGGAGGCTCTAGCCCCTGTCATCCCCTAGAGCTGCAGACTTCATAACCACTAGCTAGCTCCCTGTCTGCACCCGGGTGTTGAAGGCCTCACCTCACTGTGGGAGCCCCACAGCCAGACTCACCTTCCTGTGCCTTCTGTGCAGCAGCCAAGATCCCTCTGCAAACCAAACTACACCTCTCCTAGCCTGTGTGCCCACCAGGAACTTCCTGGCCCCGAGGGTGCTCAGGCCCTCCCCATCCCCGACCCCTCTCCCTCTCTTTTTTTGTATATATACTGGTCATTTTCAAGGGAATGCCTGAGGGATGAGTGTACTGGTTATGGAGGAACTGGGGGTGGGGTAGGGAGGTCCCGTGTTTCAGTGCAGTGAGAAAATAAAATGAAAGGCTGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=FE(21.3=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGATGGTGTTGTGACCTT
R:
TTCCTGGTCTTAGCCCTGAGC
Band lengths:
351-955
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: