MmuINT0042879 @ mm9
Intron Retention
Gene
ENSMUSG00000060924 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:MGI Symbol;Acc:MGI:2137383]
Coordinates
chr8:15999780-16000626:-
Coord C1 exon
chr8:16000481-16000626
Coord A exon
chr8:15999861-16000480
Coord C2 exon
chr8:15999780-15999860
Length
620 bp
Sequences
Splice sites
5' ss Seq
ATGGTCAGT
5' ss Score
6.57
3' ss Seq
TTTTCATAAACATACTACAGCAT
3' ss Score
3.08
Exon sequences
Seq C1 exon
GGATGGTCCTGACCAGAACTCGCCTCAGCTCGGGGTCTTCAGTGGAAACACTGCCCTTGAGACAGCCTACAGCTCCACCAACCAGGTCCTGCTCAAATTCCACAGCGATTTCTCCAATGGAGGCTTCTTTGTCCTCAATTTCCATG
Seq A exon
GTCAGTTTGTTTCCACTTCAATGGCTGTGGCATAGAGTCCCAGGAAAGCTCCCTACCCTATATCCATACTTTATCTCCAGCTGTTGGATTATCTCACATGTCCGCCAGAGTGTCCTGGAAACCTTTGGTGGTACGAAGTATCTCTACTGTCAGCTCATTTCATCAGGTCGTGTTGGTAGATACCTGAGGTTCATTCCTATGTAGATGTAAGAGAGATCCTGTTGTAGACACCATTGTGATGCACGTGGCTTATGTGCAGGCTTGTGTGTGCCTGACTCTAAAGAAATGTCATAGTAACCATCATATAATGACCTCATGATGTCTTTGATAGCAGAAGGGCAAGGTCGCCAGCCCCTTGTCTCCTATGACCCCAAAATGTTACTCAAGACAAGAGAGAGATGAGCTTATCTATGCTAAACAGTATGTGGTAGGATGATTTCAGTGATGTCTTCCAAAGTGGGGAGGATAGGTGTCATAGTAACTGCATGATTGTCGGGCATATAATAGCCAGAGAGAGCCATTGGGGACAGTGATTTACACATGCACGTGGCCTTGTAATTTGATCACTCAGGAAAGTTAGTTAACCACAGCTGTTATCTTTTTTCATAAACATACTACAG
Seq C2 exon
CATTTCAGCTGAAGAGGTGCCCGCCTCCCCCAGCAGTGCCACAGGCTGACCTGCTTACAGAAGATGAGGACTTTGAAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060924-Csmd1:NM_053171:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.143
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(44.2=92.0)
A:
NA
C2:
PF0008415=Sushi=PU(36.2=75.0)
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:
GTCCTGACCAGAACTCGCCTC
R:
AAGTCCTCATCTTCTGTAAGCAGG
Band lengths:
214-834
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: