MmuINT1007717 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128393490-128395090:+
Coord C1 exon
chr4:128393490-128393705
Coord A exon
chr4:128393706-128394901
Coord C2 exon
chr4:128394902-128395090
Length
1196 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
CCCACTGTCTTCCTCTGCAGAGT
3' ss Score
11.96
Exon sequences
Seq C1 exon
GCGTGTTCTTTACTTTCCATACCTTCCACCTGGAGAGCGGCCATGACTACCTCCTCATCACTGAGAACGGCAGCTTCTCCCAGCCCCTGAGGCAACTGACCGGCTCGAGGCTGCCAGCCCCCATCAGTGCCGGGCTCTATGGCAACTTCACCGCTCAAGTCCGCTTCATCTCTGATTTCTCCATGTCCTATGAGGGATTCAACATCACCTTCTCAG
Seq A exon
GTAATGTGTGTGACTGTCCCTGGGGAGAAGAGACCAGGGAGCCATTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCAGCTCTTCAATGACCTCAATGCTGCAGGTGAAGATACTTAGCTTAGACACAAGGATGGACTTCACGGGAACAGTCTTGACGTGTGTCAGGAGGCTCATTCTCTGACTCAGGATACACTTTGAACATGCCCCCCCCCCATACACACACACACACACATGGCTGAACTAGAGGAATTCACAAGAGTCCCTTCCTTCTTCAAGAGTCCCTGCTTGACGAATTTCCCATGACTCACTCCTGTTTCACAGCCCCAACAATTATAGAAAGAGATGAGAGTCACTGTATCTGTGTTTCAGTCCCATTCAGCATCTGCATCTACGCTAATCTCAGAGTGATGTATTTTTAGCTCTGGATTTGGGAATCCTGAAAAGAAGGCTCTTTCTTGGCATTTGAAACCTTTACTCCTGTTACCAGCTGTCCCCTCCACCCTCATCCTGAGGTACCCAAGGTCTCCCGCATCAGCAAGACAGAAGGACTGATGGACTCCTCCTTAGCCCAGCTTAGCCTCCTGCTGCCCTCTGAAGTCCCCAGGCCACCAGCCTGAGCTGGCCTGGCCAGTAGGACCCTCCTCCCTACTATACAGAGCACGGAGCATCGAGAGACAGTCACATCCTCACTAAAGACATCACGTATGCCCTTGGCCCATCATTGCCACCTACCCTCCCACTGGGCTTATCATTGGCCACAAAGCCAGCCTTGTTCAGAGAAAACTTCAAGAGAAGCGTTTGGAGTCAGGATCCTAGTGCAAGTTGCTCAAAGCAGGATCACAGATCCTGACTCCCTGAAAATGGCTGGTTGTGTGAAGCTGGTTGGTGCCTGGGGAAATTCCAGAGCACCTGCCAGGCCCAGGTTTCAGGTTCAAGTGGAACCCCAAAGTAGGGGCAGAGGGAGGACTCTCAAAAGTCCTCTGTGGAGCACTTCTCCCAGATTCTGAGCCTCCCAACATTTCTCTCAGCCTGAGCCCTCAGGATGGCTCTCCTTTTCCCCACACTTGTTGGGAGCTAGCACGCTGTAGTCTCGGATTTTTTTCCTCTGGTCCTTTTCCCTGGTGCTGGGGCTGTCCTCAACTGTCTCCAAGACTAACACTCCCACTGTCTTCCTCTGCAG
Seq C2 exon
AGTATGACCTGGAGCCCTGCGAAGAGCCCGAGGTTCCAGCCTACAGCATCCGAAAGGGCTTGCAGTTTGGTGTGGGCGACACCCTGACCTTTTCCTGCTTCCCCGGGTACCGTCTGGAGGGCACGGCCCGCATCACGTGCCTGGGGGGCAGACGGCGCCTGTGGAGCTCGCCTCTGCCAAGGTGTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:20
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=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(64.8=95.9)
A:
NA
C2:
PF0008415=Sushi=WD(100=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCACTGAGAACGGCAGCTT
R:
CAACACACCTTGGCAGAGGC
Band lengths:
350-1546
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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