MmuINT0042905 @ mm10
Intron Retention
Gene
ENSMUSG00000060924 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:MGI Symbol;Acc:MGI:2137383]
Coordinates
chr8:15900673-15902202:-
Coord C1 exon
chr8:15902115-15902202
Coord A exon
chr8:15900806-15902114
Coord C2 exon
chr8:15900673-15900805
Length
1309 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
AAATTCCTTTTGTCTTCCAGATC
3' ss Score
9.7
Exon sequences
Seq C1 exon
GTGTCCTCAGGACTTGAGAGGGGAGGATTCTCCTTTCAGGGTGATATACATGGAAAAGATTTTGGGAAGTTCAAGCTGGAAAGACAAG
Seq A exon
GTAAACTTACCTATTTTTTGTTTGTTTATTTGTGTAAGGCAAAGCTCAATTGGGTCTACACTCACTGATAAGTGGATATTAACCCAGAAACTTAGAATACCCAAGATACATTTGCAAAACACAAGAAAATCAAGAAGAAGAAAGGCCAAAGTGTGGATACTTCATTCCTCCTTAGAATAGGGAACAAAACACCCATGGAAGGAGTTACAGAAACAAAGTTTGGAGCTAAGATGAAAGGATGGACCATCCAGAGACTACCCCACCCGGGGATCCATCCAATAATCAGTCACCAAACCCAGACACTATTGCATATGCCAGCAAGATTTTGCTGAAAGGACCCTGATACAGCGGTCTTGAGTGAGGCCATGCCAGTGCCTGGCAAATACAGAAGTAGATGCTCACAGTCATCTATAGGATGGAACACAGGGCCCCCAATGGAGGAGCTAGAGAAAGAACCCAAGGAGCTGAAGGGGTCTGCAACCCTATAGGTGAAACAACAATATGAACTAACCAGTACCCCCAGAGCTTGTGTCTCTAGCTGCATATGTAGCAGAAGATGGCCTAGTTGGCCATCATTGGGAAGAGAGGCCCCTTGGTCTTGCAAACTTTATATGCCCCAGTACAGGGGGACGCCAGGGCCAAGAAGTGGGAGTGGGTGGGTAGGGGAGCAGAGCAGGGGGAGGGTATAGGGGACTTTGGGGATAGCATTTGAAATGTAAATGAAGAAAATATCTAATAAAAGGAAAAGTTTTAACAAAGAGGCAGAGAGATTGGAGTTCAGACTCTGCTGGTAGGGATGCTCAGGCGTACAACTTCTGTGCAAGCAACATGCAGCTCATCCGAAATGCACATAGAGTGACAGAGACAGAGAACTGTGCCCCTGCTTGTCCAGCCAAGGGAACTGGAAGCAGGTTCTTACACATGTGTCCCAGAGGCTTTAGGCATGTTATCATTACCGCTCAAGAGGAAACTTCAAAAGTCCATCAATTGAGGAGTCAGAGAAATGTGGTACATACATTGATACAATGCAGTATCAGTCAACATTAGGAAAACAATGAAATACTGATGGCTGACACACTCGAGATGACTTGTGAGCCATGAAAATTCTAGAAGATTCCATTTGGATACCATGCTCAGGAAAGGAAAATCTACTGAGAGAAAGTTTGATGAGCAGTCTTCAGGAAAGAATACTGGGTTGCTTCACCATGGGAGGGAAACTCTGATTTTTGTGCTCATCTCTAAGACAATATTATAGACACTCTTCAGCCTAAGAAGTATACAATGGCTCCAAATTCCTTTTGTCTTCCAG
Seq C2 exon
ATCCTTCCAACTCCGATGCAGATTCTTCAAATCACTACCAGGGCACCAGCAGTGGCTCGGTGGCAGCTGCCATTCTTGTTCCCTTCTTCGCTCTAATTCTATCAGGGTTTGCATTTTACCTCTACAAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060924:ENSMUST00000082104:68
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.067 A=NA C2=0.311
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGGACTTGAGAGGGGAGGA
R:
CTGTGTTTGTAGAGGTAAAATGCA
Band lengths:
215-1524
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