MmuINT0028729 @ mm10
Intron Retention
Gene
ENSMUSG00000043705 | Capn13
Description
calpain 13 [Source:MGI Symbol;Acc:MGI:2685789]
Coordinates
chr17:73339342-73341149:-
Coord C1 exon
chr17:73341075-73341149
Coord A exon
chr17:73339488-73341074
Coord C2 exon
chr17:73339342-73339487
Length
1587 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATT
5' ss Score
5.73
3' ss Seq
TGTGTGTCTGTTTTCCACAGGAT
3' ss Score
12.59
Exon sequences
Seq C1 exon
GTCCAAGGAGTGGAGAGAAACCCATGACCCACGGAAAAGCCAGCTGTATGAGAACAAGGAAGATGGCGAGTTTTG
Seq A exon
GTAATTACCCTTCTTTAAGGATGTTTGGAGTATTTATTTCTCAAGCCCTCCATCCCAACTGCTCCTTAAACTTGCACGAGGATGGAAAGTAATGTTGCAAAAACCCACACAGAGGGAACCTATAGTCTTTACCAAGTCACAAAAGCTTTGAGTGGCAGGCGTTATGGCCTCCCTTCTGGATGTGAAGGTTATCTTGGAGATGAGAGACTGGGCTCTCCTGGAAGCCCAGGGAGGGGAAGGGCTAGTTGCTCAGAAGTTTGGATTTGGAGGTATGATTGTCAACCCTGTCTTCCATCATCTGGGGACACAGCAGCTACAGTTTGCTTTGACAACACTCTGCAACAGAGTAACTGAAAGTGAATCTACCAGCCTGGCCCTGGGTGGAATATCATTGTCCTTGATTAGACGCTATTCAGCATTCCATGTCTTGAAAGCACGTGCCATGTCTTATGTGCACATCCTACAGAAGATGGGCGTTTCTTGGGTCCTCTGGTTGGCTTAGTGATGCATGGTAGCGAGACTTAGCATGTGTCCATGAAAAGGATGGGAAGCAGCTGGACAGATCTGTACAGCGAGTGTGGCTGGGACCTTGGATTCTCCCTGGAGAACAGGAGAAAGAAAGGGAACTGGAGAGAGCTTGGCTATGACAGCACACACAAGACCTGCACAGGTTCAAGCGAAACAAAATCTCAGCAGTGGGAAGAGGACGCAGACACAAAGCCCCACCCTTAAGCAAAAGCTGTTTTCTCCAATGGAGTGTCCATAGGCCAGGGTAAGCGCTTTGCCAAGAAGTAGCAGACCAGAATAAAATCAACCCCACTTTGGGGTGTGCTTTCTGTTTTGTTTTCATTTGTTTGTTTTTTAGTTGTCTGCTTCGGGTTTCCCTTCTTGTTGTGTTCATCTTTTGTGTAAGAAAGAGGAAGAACATAGTGTTGGGGACATAATGTTGTGGAGGTAGGTGGGCGGGGAGGAGCTGGAGGAGGAGTGAGAACACAGTCAAAATATACTGTATGAAAACAAATTCAAATCATTTTTAAAAGAAGACATTTAGCATAAGTGAGATACGGAAAGAAAGTCTGGGTCTGAGTTACTCAGAATCAGAGAGACAAATGTCAATTAGAAGGGCAAATCTTCCTCAATATCTCTAGGTTAATCCTAGCAAAAGGCTAGGTTTTCACTGTGGCATCCATGTGTTTCTTTAAAGACCTCAGCAATAAGTTTGCAATGAGCAAAGGCAAGATTGCTTGCTAACAGTTCGAAGGACTAAGAGCAGAGAGAACCTGGCCTTTGTCCCACTGACCCTAAAAGGACTTGGTTGGATTAATGGGTTTGGAAAGTAGTTTCGCCAGGTGACACACAACACCCAGTCTTGTATCTGCTACTGTCCTCTCCAGCATTGGAGGGTAGTCTCAGGGCGAAAAGGCATGACACTGAAGGTGCCAGAGATAAGACTTTGGTCTTTGGGAAAGCCTATGGTAAGTCACACATGGGGACTTCCTCTGATTGGACAGATGTAGGGAAGTGGTGGGAAGCTGGAACTGAGGACACGGCCGGAAGTGACTTGGGCTGTGTGTCTGTTTTCCACAG
Seq C2 exon
GATGTCCTGTCAAGATTTCCAGGAGAACTTCTCCTGCCTGTTCATATGTAACCAGATCCCGATCACCATGGATCATGGAGTCACACCCAATGAGAGCTGGCGACAAATGAGGTTTACAAACCAAGTGATCTCAAGAAACAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043705:ENSMUST00000095208:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=38.0),PF0106717=Calpain_III=PU(13.1=36.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAGTGGAGAGAAACCCATGA
R:
GCTCTGTTTCTTGAGATCACTTGG
Band lengths:
214-1801
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