MmuINT0042894 @ mm9
Intron Retention
Gene
ENSMUSG00000060924 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:MGI Symbol;Acc:MGI:2137383]
Coordinates
chr8:15921034-15921905:-
Coord C1 exon
chr8:15921729-15921905
Coord A exon
chr8:15921214-15921728
Coord C2 exon
chr8:15921034-15921213
Length
515 bp
Sequences
Splice sites
5' ss Seq
CAAGTCAGT
5' ss Score
2.74
3' ss Seq
TCCTGTCAACTACCTCTTAGTCA
3' ss Score
3.47
Exon sequences
Seq C1 exon
CCGTGTCCTGCGGAAACCCAGGCACGCCGACCAACGGGATGATCCTCAGCAGTGATGGGATCCTCTTCTCCAGCTCTGTCATCTATGCCTGCTGGGAAGGCTACAAGACGTCGGGGCTCATGACTCGGCACTGCACGGCCAATGGGACGTGGACAGGCACAGCTCCTGACTGCACAA
Seq A exon
GTCAGTACATGCCCATCTGGAGGGGCTGGAAGCTAGCCAGTTGAAGGAGACAGTGGAATTTTCAAATTTATTAAATCTTTTTAAAAAAAATCATGCAGAATAAAGTATAACATAAGTTGGATGAGATGCTCTGTTTTTTAGACGCTTTAAGATTCTTTAAGCATCTTTAACTTACACAATGAAAGTATGGAAAATTAGGCTATGTAATGAAGGAAGAACCAAAGAGACTCTAGACCACCTAGTTTAAAAAGAAATAAGCTACTTTGTACTTGTCCATAGCTATAGGTGTATCCTGATCAGGCACGGCCAGGGGTGACAGCCTTACTGCCACCTATTAATAGAGCAGCAATTAACAATTCCAAACACAGCCACTTGGCAGCAGCTCTGTGGAATCTGTGCCCTGTGGCTGGTCACCTCTCAGTTCCGCACTGTATCCCAGAAGAGTGCTCACACAGTTTGGTTCCTGTCACGGTAATTTGCATCTCTCTGCTTCTTTCCTGTCAACTACCTCTTAG
Seq C2 exon
TCATCAGCTGTGGGGATCCTGGCACACTGCCCAATGGCATCCAGTTTGGGACAGACTTCACTTTCAACAAGACCGTGAGCTATCAGTGCAACCCCGGCTACCTAATGGAGCCCCCAACATCACCCACCATCCGCTGCACCAAAGATGGCACATGGAATCAGAGCCGGCCCCTCTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060924-Csmd1:NM_053171:58
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.7),PF0279317=HRM=PU(82.5=55.0)
A:
NA
C2:
PF0279317=HRM=PD(15.0=9.8),PF0008415=Sushi=WD(100=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCCTGCGGAAACCCAG
R:
CCGGCTCTGATTCCATGTGC
Band lengths:
342-857
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: