MmuINT0042937 @ mm9
Intron Retention
Gene
ENSMUSG00000022311 | Csmd3
Description
CUB and Sushi multiple domains 3 [Source:MGI Symbol;Acc:MGI:2386403]
Coordinates
chr15:47585261-47587027:-
Coord C1 exon
chr15:47586932-47587027
Coord A exon
chr15:47585465-47586931
Coord C2 exon
chr15:47585261-47585464
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-Csmd3:NM_001081391:34
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.006
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
Rat
(rn6)
No conservation detected
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]
Other AS DBs: