MmuINT1007733 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128474798-128475813:+
Coord C1 exon
chr4:128474798-128474922
Coord A exon
chr4:128474923-128475716
Coord C2 exon
chr4:128475717-128475813
Length
794 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTGTCCTTCTGTCTGTCCAGATT
3' ss Score
9.66
Exon sequences
Seq C1 exon
TGCCGTGTGGTGGCAACCTCACTGAGCGCAGGGGCACCATCCTGTCCCCTGGCTTCCCAGAGCCATATCTCAACAGCCTCAACTGTGTGTGGAAGATCATGGTCCCGGAAGGCGCTGGCATCCAG
Seq A exon
GTAGGAGCAAGGAGGCGCCTTAGTTAAGTGGCTGCTGTTAGACTGAGGTGGAGGGAGAATCAACAGCTCCATCCTTGTCCCTGGGTCACTGGGAGCACATTTGCAGATATAGAGATATGACTCCAAATCACAGCATCTCTGGGGGGAGGGAGGATGAGAGAGGAAATTAGGTCCAGCCAGCCAAGAGGGCCCAGAGAAGAAAGTGGGCTTACACCTGCAGTGTGACTTTGGAAGGTTCTTAGGAGACATTCAAATGGTTTGAGGCGTATCTAAGATCATTAAGGAGAGAAAAGCGATATCACTGATAAATGGGGGAGGAACAGACCAGCAAGTGCAGTGAGGCCAGGGGAGAGCATCTGGGCACACATCAGGCTACGTAACATATGCCCAGGGCAAGGGCAACACAAGGAGACATGGGAGAAGAGCCAGAGCCTACCAGGCCAGTGAAGCCATCAGGACCCCAGCTGGACACACCCAGTGGGAGAAGGAAACCCCAAGAATATTCCAAGTGGGAGAAGGCAGCTCAGATGGTAGAGTTCTTTCATGACATACACAATGCACTGGGTTCAATCCCCAGGTGTGCTTGTGCACACCCATAATCAGCACCCCCAGGAAAGCAGAGGCAGGGGGATTAATAGCTTAGCCATCCTCAGCTACATAGTGATTCAGGATTAGTCTGAGCTATGTGAGACCCTGGCTCCTAAATAAATGAATAAATAAATAACCCACGGGAAGAGTCAGGAGGGAGGCACTTGAGCTGTGTGACCGACAACTCTGTCCTTCTGTCTGTCCAG
Seq C2 exon
ATTCAAGTCATCAGTTTTGTCACAGAGCAGAACTGGGACTCTCTAGAAGTGTTTGACGGAGCAGATAACACCGTAACCATGCTGGGGAGTTTCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:35
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:
PF0043115=CUB=PU(36.8=92.9)
A:
NA
C2:
PF0043115=CUB=FE(30.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGCAACCTCACTGAGC
R:
CCGAGAAACTCCCCAGCATG
Band lengths:
214-1008
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