MmuINT0028768 @ mm10
Intron Retention
Gene
ENSMUSG00000079110 | Capn3
Description
calpain 3 [Source:MGI Symbol;Acc:MGI:107437]
Coordinates
chr2:120504096-120504913:+
Coord C1 exon
chr2:120504096-120504154
Coord A exon
chr2:120504155-120504472
Coord C2 exon
chr2:120504473-120504913
Length
318 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CTCAGGGTTTCTTCTTCCAGTGG
3' ss Score
6.67
Exon sequences
Seq C1 exon
GAGCTTTTAACGCATTTGACAAGGATGGCGATGGTATCATCAAACTGAATGTACTTGAG
Seq A exon
GTAAGTGCAGCAAACACATCCTCTGCACAGAACCCACAGGGGGTGGGAGGGATGAATGACAGGCAGAACCCAGCACGCTTCTCACTCTCAGGACTGGAACTTGGTGAAGATTGCGATTCCTGGGGTGGGTGTACAACAGAGGCTAGCCCCACCTCTGAGTTGCACCTCGGTGGAAGATACTTTCCTAGGGAAGACCCAGGGAAGGCAGGCTGCTCCTTTAAGGCTCCTCCCTTTCTCCGTCCCAGCACAAGCAATTCCTAGGGATGGCTGTTACCTCCTTGTTTGCTCTTGTACTGATCTCAGGGTTTCTTCTTCCAG
Seq C2 exon
TGGCTGCAGCTTACCATGTATGCCTGAACCAGACTGACCTCATGTTAAGAGCAACTAGGATTTCATCTCAACACAACACAGCTAGAGCCATCTACCACAAAAGACCCAGTAGGTGCATCTCCACCAAACCTAGGGGGCTCCTGGTCATGTTCCTTCTCCATTTTGCACCAACTCTTGGTGCACAGCCTGATGCCACCTGAAGTGTCTGGCTTGCTGAGAGGTCTGTAGATTCTGAAACTGTCTACTTAGCTTGTACTGGGTTGTCCATAGCACCTGTAGATGGCTCTCACTCACGGAGGAGCCCAGTCGCCATCTGCACTCAGTTCTGCCACTTTTAGGGTGGGTCTATTCTGGGGTCAATAGGGCGTGGATATCTGACAAAAATGTGGCTACATTCTGAAAGAAGCTATCTAAATAAAGGCACACACATGGCTAGTTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079110:ENSMUST00000028749:23
Average complexity
IR
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(20.7=100)
A:
NA
C2:
PF134991=EF-hand_7=PD(3.3=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGACAAGGATGGCGATGGT
R:
CTCCGTGAGTGAGAGCCATCT
Band lengths:
343-661
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types