MmuINT0028860 @ mm10
Intron Retention
Gene
ENSMUSG00000001794 | Capns1
Description
calpain, small subunit 1 [Source:MGI Symbol;Acc:MGI:88266]
Coordinates
chr7:30193878-30195164:-
Coord C1 exon
chr7:30195006-30195164
Coord A exon
chr7:30194102-30195005
Coord C2 exon
chr7:30193878-30194101
Length
904 bp
Sequences
Splice sites
5' ss Seq
TCCGTAAGT
5' ss Score
10.27
3' ss Seq
CCACCCCTTTTACTTTACAGGAC
3' ss Score
10.89
Exon sequences
Seq C1 exon
GCGCAGTCTGCAATGGAGGCTCTAGGACCGCGCAGACGACGGCTGGGTGGCGGCAGGGTCTAACCCGGAGTAGCTGCCTGAGTCACCGGCCCCGCCCTCCCGAACCGGACACAGCGGAGGCCCTGCAGCAGGCGAGCAAGACCGCGGACCGCCGGATCC
Seq A exon
GTAAGTGAGACGGGACACTCCAGTCCAGCACCCCTGCACCCTGTAGATCCGGAATCCGTAGTCCTCAGATCTGGCGAGACCCTAAAGTCTTGGCCCTTGGGGGGTCCTAGGACCGGTGTTCTCAGATTCGAACCATCGGGCCTGTCAGCCCCTCCAGAACACTCCTTACCATCCCGGATCTGACGACCAAAAAATATAAGCCCAAAGATCAGAGAGATACCCGGAAATTATTTTGGGCGTCTAGAACCACAATCCGAGATCGTGGTTCCCATTTGCGGTGGGAAGAACTCCGTTATCCAGGATCCTCCGGGCGCACAGCCATAATTTTTGGCCGGAGCCCACAGATCCCGTAGTGACAGTGTAGTCCCTCTGTCGAGAGTATCTGAATGTCTTAATCCACATTAGGAACTTCCTGGTCAGCCCTGGGTCATCCCTACCCTGAGCTTAATTTTGGAAGGCCTGGATCTGAGACACGTTCGGTTTTACACACCTTAGGGTTTCTACACGAGAATCCCCTGTTTTCCCGCTGCCTCAAGACAGGGTAAAGCAGGCAGGCGCTGTAGCCGAGGCTGGCCTTGAACTGGTCCTCCAGCCTCAGCCTCCCAATTTCTGGGATTACAGTAGAGCGCTACCACGCACGCCCAGCTGTACCCCTGTCCTCATGCCTATATATATGCAGTCAAGCCTGGGCCAGGGTACTTTCTAGACCCTAGGAGGTTTCACATCTCCTATCACCTGTCCAGACCCCTAGCTAGAGGCTCTGTCCCCATCTCGAGGCCTTAGTTTCCTCCCCAATCTAGTTGCCGGAAATGCTTGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCGGGAAGGGCTGGGCTCCTGGCAAGGCCACTACCCGACCCACCCCTTTTACTTTACAG
Seq C2 exon
GACTCAGCTGCGATCATGTTCTTGGTGAATTCGTTCTTGAAGGGCGGCGGTGGCGGTGGGGGAGGCGGGGGTCTGGGCGGGGGCCTGGGGAATGTGCTCGGAGGCCTGATCAGCGGAGCTGCTGGCGGCGGCGGCGGTGGCGGTGGAGGCATGGGACTGGGAGGAGGTGGCGGAGGCGGTGGAACTGCCATGCGCATCCTGGGCGGAGTCATTAGCGCCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001794:ENSMUST00000001845:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.114
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGACGACGGCTGGGTGG
R:
CTGATGGCGCTAATGACTCCG
Band lengths:
351-1255
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