MmuINT0042878 @ mm10
Intron Retention
Gene
ENSMUSG00000060924 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:MGI Symbol;Acc:MGI:2137383]
Coordinates
chr8:16000481-16002692:-
Coord C1 exon
chr8:16002515-16002692
Coord A exon
chr8:16000627-16002514
Coord C2 exon
chr8:16000481-16000626
Length
1888 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGA
5' ss Score
5.27
3' ss Seq
CGGCCCCATCTCTTTCCCAGGGA
3' ss Score
8.64
Exon sequences
Seq C1 exon
CTCCCTGTGGATATAATGTGACATCACAGAATGGTACCATTTATTCCCCTGGGTTTCCAGATGAGTACCCAATTCTGAAGGACTGTCTGTGGCTGGTCACTGTCCCTCCAGGCCACGGAGTGTACATCAATTTCACCTTGCTGCAGACCGAGGCTGTAAATGACTACATTGCTGTGTG
Seq A exon
GTATGACTTCTCTCTCCCAGGGAATGGCAGCTCCTGCTGGTGGTGGGATGTTTCAGCTGAACATTCGCTTCTGATTTGTAAGGTTACATGTTTACCAATGATCTGTCTGGGCACATCTTGAAAAACTAATTCATCAACAAAATCAAACAATAGAGAGGACATTTCAAGGCATATGTCTAGTTTGCTATTAGAAATAATGAGACTGTTTGAATGTACTGGGGAAAGTTGTGATTACTTTATTTCATATTTTGCTTTGCTTAAATTATTCGTAATTTTTTTTTTAAAAAAATAAGGTAACCTAGGCTAGCCTTGAACTTGTGACCTTCATGCCTCAGTCTCCTGAGTGCTGGAATTGCTGTTGGGTGTCATTTCATCTGGCTTACTCCACAATTTTAAGGGATGTGTGTACATGTGTGTGGGAATGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGTATATGAGGACAATACACACACACACACACACACACACACATATATACATATACACAGACATATATTTCCCTTTAATGAATTCATGAGAGAACACTAAGGAAGTATTTCCTCAGGGCATCCTCCTACCCTGAATTGCACAGACCTGGTTTCCCATGAGTCTTGGAGAGAAATCTAGGCCAGGATGTGATGAATATGAATCTACTAGATGGAACCTGTAGAAATTACCTGTTCCACCAAAGAGATCTTGGGTGTTATTTAAAGGCAAAGATGGTATGAATAATCTCCCTTATACTATAATGGGAGAGCCAGGAGGTGCTGATGGGGTACTGGGAGGATAGCATTGTTGAATTTACAGGTGAACTGTGTATGTACATTTCTGATGTATGATACATGAAGTGTATGTATTTGTAGGTATGTGTCTCTACATGTGTGGCTTATCTATGATTGTATTTGTGTTTATGCACATTTGTGTTATATTCCATGTTTGTATGTCTGTTTATAAATGAATACTTATTCTATGCATGTATATATACATCTCTGCTTGTGTCTGTAAATGAATGTATGATTATGTGTGTGTGTTGTATGTATCTGTATGTGAATGTAGAATGTTTTATATCTATATTGTGTCTGTGAATGTGTGTGTCTGTCTATTGAGTGTCTAAATGTGTCTGCCTGTGTGTAATATATGTGTGCATGGAGGGTGCATCATGTGCCTATATTCTTATTACAGGTCAAGGAGTAAGGGAGAGTAGCCTGGGTCAGAGGAACAGGCACTAGATAGCCTAAATATTTCATCTAAAATGCAGGAAGAGCCATACACAGGAGAGCCAATGTGGATGATGCTCCTGCAGGGCTCAGGGGAAGCTGCCTCGCCAGGCTGCAATGAGGTCTTGGCGGGTGGTTCTGAGAAGCTGAGCTAGTGGCTGTGGAGATGAAGCACCATGGGTTCCTTCCTGTTCCAAAGCGAAGCAGTGAAGCAGCAGTCCCACCAAGCAATAGATCCATGTAGATTCCGCTGCATAGAATCCAGTCGTAGCAATTCATGTGTGTCAACTGCCCACAGTCAGAAAGCAGAGAGATGTTGCAGGGTGGTGAACATCCTAAACACCATGCATGCATCCTATTACTAAAGTCAGTGCCAGGGAAATACCACATTTCAATGTTAGTATTTTAATTCAACTGTAAAACTTATTATAAATATCAGTCATAAGGAAGTGAATACCATATGTATTTTAAAATGTAGTTGTTGTGTTCCTGACAGTACAGAAGTATCTCTGAGGAGGCCAGTGTGCACTGGTCTTTCTAGATCAGCCCTGTATTCTTTCTGTACACTTGGCCCTACTGGGAAACTGGCTGCGCAGCCTCTGCTATAACATTGAACTTACTCCTCTCACGGCCCCATCTCTTTCCCAG
Seq C2 exon
GGATGGTCCTGACCAGAACTCGCCTCAGCTCGGGGTCTTCAGTGGAAACACTGCCCTTGAGACAGCCTACAGCTCCACCAACCAGGTCCTGCTCAAATTCCACAGCGATTTCTCCAATGGAGGCTTCTTTGTCCTCAATTTCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060924:ENSMUST00000082104:43
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=0.020
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(54.8=95.0)
A:
NA
C2:
PF0043115=CUB=PD(44.2=92.0)
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:
CTCCCTGTGGATATAATGTGACA
R:
AATTGAGGACAAAGAAGCCTCCA
Band lengths:
318-2206
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