MmuINT0028851 @ mm9
Intron Retention
Gene
ENSMUSG00000031981 | Capn9
Description
calpain 9 [Source:MGI Symbol;Acc:MGI:1920897]
Coordinates
chr8:127141333-127142631:+
Coord C1 exon
chr8:127141333-127141391
Coord A exon
chr8:127141392-127142381
Coord C2 exon
chr8:127142382-127142631
Length
990 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
TCATCTCTCTTTACTTCCAGTTC
3' ss Score
9.6
Exon sequences
Seq C1 exon
GGGTGTTCCAATCTCTCAGTGTGAAGAACAAGGACTTCATCCATCTCAACATAAACGAG
Seq A exon
GTATGGCCAAGCAGACCCCGGCCAGGGCGCAGCAGAGTATGAACACGCTAAGTGGATCCCCCAGGCAGGACGAGCGAGCACTCGCCGTGGGCAATTACTCAGTGCAGAGGCCGGTGTTTGTCCTTTTGGCAGTCAGCATAATTAGCGCTATAATCCTGTGAGCTGTGGGTGTCTTCATTGCCCTAGTGTCTGCTCATGTGAGCCCCAAGAAAGAGGGTGTGGAGTAAACAACGTTCCACATAAACACGAGCAAGCCTGGTGAGAGGAAGGGAGAAATGAGAAGCTTCCAGCTGCTTCCGCAGCCTGGCAGCTCGCTTGCTCACAAGGAGCCTGAGCTACCACCCTGCCTCCCTTCCCTTCAGCTCCACTATGGTAGAGGGCCATCTTTCTCTGGAAAGGTGGGTCACCAAACTCACACTACCCTGCCCAAGATGTCTCTGTGAGGCTTCCCCTTCAACAGGAACAAAACACATCTTATCCCTTTGTCCTATCCGCCCTCTACTGAAAGTGCACTTAGCCTTTTTCAAGGTTTATCTGACTGGGGAGATGGGCACAAGCAGAAGGGCCCACGTTTGAACCCTACGACCCGTGTAAAAAGCCAAGTCTGGCGGCATGTATCTGCAATTCCAGCGCTGTGTGGGGGCTGAGGCAGGTGGATCTCTGAAGCTCACTGGCCAGCCAGTGTGGTCATGGACAATTAGTACCTACAGGTTCAGTGAGAGACTTTTTCTCGAAATAGAAGATGGGGAGAGAAATGCCTGGTCTGCACCCACATACACGTATGCATGCATACATAAAATAATTATACATGCGACACACCCAGCAATCTGTTTTAATTTAAATTTTAAATAAATGGTTTCATGTTGAGTCAGAAGGCCAAATTTGTGCAAGATGACCGACCAGCAAGAGTTCTTGCGACATAATACAAACAGAAGCCACTCCTCAGTTGCTAGGCTGGATTTCTAAAGCCTCATCTCTCTTTACTTCCAG
Seq C2 exon
TTCATCAGCCTGACCATGAACATCTGAGGTTGCTCTGACCCGATGCCGTCTGCCCCTCTGATACTCAGCTTCTGGATCATGAACCTCGAAACTTTTTTTTAGAGGGCTGCCCCGCCCACTGCTCTCTCTCCTCCCGGCCTCACACCACCCTCCTCCCCTCTCCATAGTGAGTTAGAAGAATCTAAAGGGATTGGCTGAGTTCTCTGATTCTGTGGAACTTCTTATAAAATCATTGCTCTACAAGAACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031981-Capn9:NM_023709:19
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:
NO
A:
NA
C2:
NO
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:
GGGTGTTCCAATCTCTCAGTGT
R:
AGGTTCTTGTAGAGCAATGATTTTAT
Band lengths:
308-1298
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: