MmuINT0042897 @ mm10
Intron Retention
Gene
ENSMUSG00000060924 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:MGI Symbol;Acc:MGI:2137383]
Coordinates
chr8:15917234-15918345:-
Coord C1 exon
chr8:15918172-15918345
Coord A exon
chr8:15917408-15918171
Coord C2 exon
chr8:15917234-15917407
Length
764 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
TTGCCCGTTTATTGTCCCAGCTG
3' ss Score
6.34
Exon sequences
Seq C1 exon
CTGTCCTGTGCAACCAGCCTCCTCCAGTGCCAAATGGAAAGGTGGAGGGGTCAGACTTCCGATGGGGTGCCAGCATAAGCTACAGCTGTGTGGATGGCTACCAGCTCTCCCACTCGGCCATCCTGTCCTGCGAAGGGCGTGGAGTGTGGAAAGGAGAAGTCCCTCAGTGCTTGC
Seq A exon
GTAAGTCTCATGGTGGAACCTGGCATGCCATCCTGGACACTCAAAGAGACACTCCCAGTCTCAGCAGCATAATGATGTGTGACTGTGGTCGCATTGTGGAAACTCTGAGACCTGAGCATGTGTGGCCAAGGCAGGTGCTGTTATGAGTCTGGGGTAGTTCAGAGATTCACCAGTGTGACCGTTAATACAATTTAACAAAGAAGAGACATTTGCTCAGATCCTGCCCAGCCACCTAAGTCAAGGGTTTATAAAGCCAAAGAATACAAGGTTCTGATTTGTTTTTGGAACAAAAAGAAGGTCAGATGATGCAAAGCTTATTTACAGAAGCAGAACAGGGCAGTAAAAATTTAACCTGTAGTATCCCTTAATAGTTGGAGGTCTCATTTTGCTTGATAGAGCTCTTAAGCACAGAGATTTTAAACTTTTAAATGTAAAGTCCGCCGTCAACATAATGCTATCCCAGTACCTTTTCTTTAGGAGTGTACAAAATCTGAAGACTCCATAGGATCTAAATAGGTTTAATAATCTAGCCTGAGAGCCGGGCGTGGTGGTACACGCCTTCAATCCCAGCACTCGGGAGACAGAGGCCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAATCCTGTCTTGAAAAAACAAAAACAAAACAAAACGACAACAACAAAAAACCTAGCCTGGTGCAGATGTGCTGAGTGCTGATATTGCCCGTTTATTGTCCCAG
Seq C2 exon
CTGTGTTCTGTGGTGATCCTGGCACTCCGGCAGAGGGACGGCTCAGTGGGAAAAGCTTCACCTTTAAGTCTGAGGTCTTCATCCAGTGCAAGCCCCCATTCGTATTAGTGGGATCCTCCAGGAGAACCTGCCAGGCCGATGGGATATGGAGTGGCATCCAGCCCACTTGTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060924:ENSMUST00000082104:60
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTGTGCAACCAGCCTC
R:
CTATACAAGTGGGCTGGATGC
Band lengths:
346-1110
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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