MmuINT1007762 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128548728-128549276:+
Coord C1 exon
chr4:128548728-128548901
Coord A exon
chr4:128548902-128549202
Coord C2 exon
chr4:128549203-128549276
Length
301 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGA
5' ss Score
6.95
3' ss Seq
GTTTCTGTGTTTTGGTGCAGATC
3' ss Score
9.76
Exon sequences
Seq C1 exon
CGGTGTTCTGCGGAGACCCAGGGGTCCCCCCTCGAGGGAGGAGAGAGGACCGAGGTTTCTCCTACAGGTCATCTGTGTCCTTCTCCTGCCACGCTCCTCTGGTGCTGGTGGGCTCCCCACGGAGGTTTTGCCAGTCAGACGGGACGTGGAGTGGCACACAGCCCAGCTGCATAG
Seq A exon
GTGAGAGGGGCTGGGGGCAGTGGCCTGGCTGCTGGGCAGCTGTGATGGGGGTGAGTGATGGCTATCTTCATAGTCTCACTTGTGGAGACAAGGTCCTTCACTGCCCTTCTTGGGACAGAGTGTAGGACAGTGAGAGCTAATTAACTAGGGAATGCAATGTCTGCGTGGACCTGAGACAAGTGGGAAGCTCAGAAGGTGGAGCCAGGAGGTAGCTGTGTCCCTTCCGTGGCCTGCAGATCAGAAGGGGGTGGGCAGTGAATGTGCCAGTGACCCTGTGATCTGTTTCTGTGTTTTGGTGCAG
Seq C2 exon
ATCCCACGCTGACCACATGTGCAGATCCTGGCATGCCGCAGTTTGGAATACAGAACAGCTCCCAAGGCTATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:61
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.080
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=PU(32.7=72.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTCTGCGGAGACCCAG
R:
CTGATAGCCTTGGGAGCTGTT
Band lengths:
246-547
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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