MmuINT0042936 @ mm9
Intron Retention
Gene
ENSMUSG00000022311 | Csmd3
Description
CUB and Sushi multiple domains 3 [Source:MGI Symbol;Acc:MGI:2386403]
Coordinates
chr15:47586932-47587627:-
Coord C1 exon
chr15:47587514-47587627
Coord A exon
chr15:47587028-47587513
Coord C2 exon
chr15:47586932-47587027
Length
486 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCC
5' ss Score
7.91
3' ss Seq
GTGTTTGTTTTGTTGAGTAGGAG
3' ss Score
4.92
Exon sequences
Seq C1 exon
TGGTGTTTGGCCAGTTTGTATTTTTCCAGACATCACTCCACGATGTTGTTGAGGTGTTTGATGGGCCAACTCAGCAGTCTCCTCTGTTATCTTCCCTCTCGGGATCCCATTCAG
Seq A exon
GTATCCTTTACTAGAACTGCCATTCATCAGCTATTGCTTAAAGACTGACTTTTGATTAGTATTTTGGAGAGAGTTGAGATCTATGTCATCCATGTTAGCAATACCATAAACTGAAAACTTTTTAACTAAGAATAAAACCACAATTTAATATTAATTAATACGCTTGAAAGAAATTGAATTATTTTCTAGGATTGTAATAAAATAAATACAATACTTAATCACAATCTGTGCTGTTTCATATGATATAAAATATTTAAGACTGAGACATATGTATTAAAATGTAATTGAAGCTTTCTGGTTAAAAAAAAAAAAGATTTCAATTGAAGCTGAACCCAAGGAAAATATATTGCTAGCAGTAGGATATTTTGAAATAATTTGATAGAACCTAGTTTGACCTTTTCAAATGAGAGTGTAAAATGATATAGTTTTTTAGGTTTACTGAATGAAGATTATTTATGATATCTGAGTGTTTGTTTTGTTGAGTAG
Seq C2 exon
GAGAGTCACTTCCACTGAGTTCAGGTAATCAGATCACAATTCGATTCACTTCAGTTGGACCCATAACAGCTAAGGGATTTCACTTTGTTTATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022311-Csmd3:NM_001081391:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=FE(35.8=100)
A:
NA
C2:
PF0043115=CUB=PD(28.3=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTGTTTGGCCAGTTTGTAT
R:
TGATAAACAAAGTGAAATCCCTTAGC
Band lengths:
208-694
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: