MmuINT1007779 @ mm10
Intron Retention
Gene
ENSMUSG00000022311 | Csmd3
Description
CUB and Sushi multiple domains 3 [Source:MGI Symbol;Acc:MGI:2386403]
Coordinates
chr15:47753715-47755481:-
Coord C1 exon
chr15:47755386-47755481
Coord A exon
chr15:47753919-47755385
Coord C2 exon
chr15:47753715-47753918
Length
1467 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ATCACCTTATTTCTATGCAGCCG
3' ss Score
7.59
Exon sequences
Seq C1 exon
GAGAGTCACTTCCACTGAGTTCAGGTAATCAGATCACAATTCGATTCACTTCAGTTGGACCCATAACAGCTAAGGGATTTCACTTTGTTTATCAAG
Seq A exon
GTAAGTGACACTGTAGTCTAGAAACACACTAAGGCTTGATGTCCATTTCCATGCTGTGCTCAGTTGACCAATATTATCCTCATAACTGTGTAGGAATGAGGAAAGTTGTTTTAAGTAGTTGTATTGATTCCTCCCCATGAATTCTTTCCCTGGAACACTGGTGCTTTATCCAACTTTTAAAAAGAATGCATTGTCCCATCACCTTTCTCAATTTAAATGTCTGATTTTCCTTCCATTCCAACATTTTGGTTCAAAAACATTCATGTTATCCTTATTATTCTTGACTCTTATCATTTTTTGTTTTTCTCATAGTCCTGTACTTTAAATTAAACATGCATACATTTGTTGTAATTTATTTAGTTAAAGTAAACATTGTCCCATGTAAACAGTATGCTTTCTCATTCTCTCAGTAAAATTGAACTTCTGAATAGCTACTAAATATTTTGTGCAGTAAATACTTAATTTTCCCACTTTTTTCTTGCCTTTTATGAACATTTTATAATGTCACTAAACTAAATCAAGACTCATTCGAGATATTTTAGATCAATTGTATATGATCATGTAATAACTCTTCTCAAAAGTATTTTGCACATTCTTACTAAGAAATATATAAACATTTGTGACACTGTATTCTTATTAAATTCCGTCATCTCACTTTTTCACATTGGTTATGGCATAAACTCTTTCCTCAAAGGCACTGAAAGAACTTATATGCATTTCTTCAAGTTATACTAGAGGGATAAATCTACTGGAATTCACCATGCCATTCTTTTGGACTGTTGTCAATCTCTTTAATTACATTTGTATGTGTTTTAAAAAGAAAAAACATCCTGTTATCATTCTACTTTACTAAATCCAAAAAGGCACAATTGATGGGCATACAAATTCTAAAATCAATCTCAAATTTGATTATATATGATTGATGAATTAAAAATAAATATTGTTGTTAATCTGTCTGACTTCTATTCTGTTTAATCTGACTGTAATTACTGAGGTCAATAGAAACAAACATACTTTGATAATTAAGTTTGTAAACATGTTTGAAATAATTAATAACAATAATAGCCAGTATAAAAAACATCTGGAATGTATTTCATGTATACTAAATTACTTTTTGCAATTGGGAAACCAAACTTAAAAATTATACATCCATTTTTGAATCTGTAAATTGCAATAGCTAAATAAAATCACTTCATTTATAGATAAGAATTTCATGAAACAAACGATAGAAAACAGCATAATTGATGTTAAAGGATCAAAGACAAATTAAAAATATCGTAAATGCCAATATCACTTTAAATTACATTTTATTTTTATCCAATTTAAAACTTTAGATGTGTTAGAATTAGTAATTCTAATTATTAAAAAAAAAACAAGAAGATTTCTTTGAGTCTCTTTAGGAAGTTACATTTTAACATCTATACTTGTCTCTTAACTATGAAATTAAATCACCTTATTTCTATGCAG
Seq C2 exon
CCGTTCCTAGAACAAGCTCTACACAGTGCAGTTCTGTGCCCGAGCCAAGATTTGGAAGAAGGATTGGCAATGACTTTGCAGTTGGTTCATTGGTCCTTTTTGAGTGTAATCCAGGATACATTCTCCATGGCTCCAGAGCCATTAGGTGTGAAACAGTACCCAATTCTTTGGCGCAGTGGAATGATTCCTTACCTACATGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022311:ENSMUST00000162830:34
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=0.003
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(28.3=90.9)
A:
NA
C2:
PF0043115=CUB=PD(11.9=7.2),PF0008415=Sushi=WD(100=94.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGTCACTTCCACTGAGTTCA
R:
CAATGCATGTAGGTAAGGAATCAT
Band lengths:
299-1766
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