MmuINT0042950 @ mm9
Intron Retention
Gene
ENSMUSG00000022311 | Csmd3
Description
CUB and Sushi multiple domains 3 [Source:MGI Symbol;Acc:MGI:2386403]
Coordinates
chr15:47507259-47508028:-
Coord C1 exon
chr15:47507948-47508028
Coord A exon
chr15:47507373-47507947
Coord C2 exon
chr15:47507259-47507372
Length
575 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAG
5' ss Score
6.93
3' ss Seq
TCTTTCCTTTTCATTAACAGGCG
3' ss Score
10.9
Exon sequences
Seq C1 exon
CTTACCAACTGAGAGTGTGCCAACCTCCACCACCTGTCCCTAATGCAGAAATCCTGACAGAAGATGATGAGTTTGAAATAG
Seq A exon
GTAAAGTCTTTTAAATAACTTGCAAAAATACCCTCATAGCAGAACTATCTTTCTTAGAAATTAATATAAAATGTACAATCGGAGCACCTGTAGGTTGATGGGATTTGTTGAGATTGTGAAGGAAGGAAAATAGTCAAAAGAAGAAAAGGAACACTAAAAACACCTAAGAATGCTGTTTTTCTAGGACATTAAAGTTTTTGTGAGCTTGAAGAAATGGTGTCTCACAATCCATGATAGAAACTTTAGTAATGAACAATAGATGGCAATCTCTAACAATATAAGATCATGCCTATGTAAAACATAGTATTCCCTTCTGGCCAGAGCATCAACGTAGCTGGTATCCATCATGAAACCTGGATCAGTAACTAATGTCTACTTTCATTCATGGTTGGACAGTGCTTTCAAGCCTCATTTGTTCAATGTTCAAAAGTTATTCCTGTTTATAAGTGATGGTGTTTTAAAACTGATTGAAATTGAGTAAATGTAAAGAATTCTGCTCCTAAATTAAAAGAGCTATTGAGCTACACTCTGCTGCAGCTTGTCTGAAGGCTTCCTTCTTTCCTTTTCATTAACAG
Seq C2 exon
GCGATATTATCAGATATCAGTGTCTTCCAGGGTTTACACTGGTTGGCAATGCAATTCTGACATGCAGATTGGGAGAGCGACTGCAGATGGATGGGGCACCTCCAGTGTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022311-Csmd3:NM_001081391:46
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 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:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAACTGAGAGTGTGCCAAC
R:
CTGGAGGTGCCCCATCCATC
Band lengths:
183-758
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: