MmuINT1007744 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128508560-128509186:+
Coord C1 exon
chr4:128508560-128508640
Coord A exon
chr4:128508641-128509072
Coord C2 exon
chr4:128509073-128509186
Length
432 bp
Sequences
Splice sites
5' ss Seq
TAGGTACCA
5' ss Score
3.96
3' ss Seq
ATGCTCGTCTCTCTTGACAGGTG
3' ss Score
11.59
Exon sequences
Seq C1 exon
CTTATCCACTCACCAAGTGCCCTCCCCCGACCATCCTCCCCAATGCTGAAGTGGTCACAGAGAACGAAGAATTCAACATAG
Seq A exon
GTACCACTGCCAAATGGCGGGGATCTCCAACCAGGGTGGCTGAGAGGGGCCAGGAAGCCATGGGGACTGGGGTGATGGCTTCGTCTCTGTAGAGGAAAACAAAGGCCCAGATCATATGGGTGGCAGTGTTCCATTAGCCAAGTGCACCCCGAAAATATAAACCCTCTTCCTTCACCCAGCCCCAGAAGGAGGAGCTGGATGTATGGCTTCCCTCTACTGTTCAAAAGCTTTAAGATAGCCTAGAATTTCTTAGGAAATATCCAGAAGGCTGAGCCGGGGAGGGAAATAGAAGTCTGGGTCATGGGGCCAGCATGGAGCTGGCATAAAGCATGACCCAGTGCTAGTTACCTTCCAGGGCAGTGGGTCTGAGGGATGCCAACCCTTCTGAACCAGACTGCTCCAGGCGATGCCCATGCTCGTCTCTCTTGACAG
Seq C2 exon
GTGACATCGTCCGCTACAGGTGCCTCCCAGGCTTTACCTTAGTGGGGAGTGAAATCCTGACCTGCAAGCTGGGAACCTACCTGCAGTTTGAAGGTCCACCCCCAATATGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(36.2=75.0)
A:
NA
C2:
PF0008415=Sushi=PD(62.1=92.3)
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:
ACTCACCAAGTGCCCTCCC
R:
CTTCGCATATTGGGGGTGGAC
Band lengths:
188-620
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