MmuINT1007758 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128544670-128546151:+
Coord C1 exon
chr4:128544670-128544846
Coord A exon
chr4:128544847-128545971
Coord C2 exon
chr4:128545972-128546151
Length
1125 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTGTGTCTTTCTTACCCTAGTTA
3' ss Score
8.32
Exon sequences
Seq C1 exon
TGATCTCATGTGGGAACCCCGGAACTCCAAGCAATGCCCGAGTGGTGTTCAGCGATGGCCTGGTGTTCTCCAGTTCCGTTGTCTATGAGTGTCGTGAAGGCTACTATGCCACGGGCCTGCTCAGCCGACACTGCTCTGTCAATGGCACCTGGACAGGCAGTGACCCTGAGTGCACAG
Seq A exon
GTAAGAGCCAAGCCCCCTGGGCTCTGTTGCAAATGGCAGCTCAGACCACCCAGCCCCTCCCTGCCGAGTAAGCTGTCAGTGGGAGTCTGGAGAAAATGATTACAGTGGAACCGTTCGAATGCCTCTGTACGTTGAGCGTATTCTCCTGTACAGCAACCATGGAGCTAAGTGCTTCCCCTCCCATGTACACACCGCCAGAATCTCACCACAGCCCTATGACGTATCTGTGCAGACTTACTCTCTGAGGATCATAGTTTATAAAAAGGGTGAGCCTAGTGCAAGATGCGCATGCGGGCATGCACCAGGATGGTGTGAGCAGGGACACAGTAGCTGTGAGCCCCACTGTTTATACATGACAGCTGAGGTTCACAGGGGCTGATACAATACACAAGCCATCATCCAGGCTCTGGTTCACCCCCTTTCTCTTTCCTTTCAGGGTCAAGGTTCTGTCATACTCTGTCCACTTTGAAGCTGACACCACCCGCCATCTTCACATCTTTCCCTATCTCACTCAGACACATCTCCACCCCAACCCAGCTTCTGAGCATTGCATCTGCCTAGCTCTTCTTTGTTGCCCCTCTCAGGGTGCCCCAGACCCTTTTCCTCAGAAAGCCAGATATTGTGGTACCCAGACAGAGGGAAGAGATGGACTGAGTAACTCTGAGATTTCTTCCTTTCAGAGTCAACTCTGTGAGCTCAGACTCCATCTGAAATCCTACATTAAGTTCATACATAGATCACCAGTCGTACCGTGTCTCATAAACGGGACTTAATTATCGCATAGGTCTTAAGACCCTGCTTCTGGGTCTGAAAAAAAAAAAGCCTCTCAGAAAGACTGTCATAGGAGATGTTGCATCCCAGGACAAGCTATCATTTTGATCCATTAACAAACACATCATATGTTCTTCAGTCTAGAAACACTCCTTGCCCAGGACCTTGCCTACTTTAGGAAATAAAGTCCTGTGGTCCTTCCTCTCAGAGGAGTGGGTTTGAACAAGAAGGGAGGCCATCGTGTAATTAGATGGCATGCATGGTATAGGCATGAACAGTGGACCTGTAGATTGAGATGCTGAGGAGACAAGGCCTGGGCTAGGAGTGACAAGCATTGTGTCTTTCTTACCCTAG
Seq C2 exon
TTATAAACTGTGGTGACCCTGGGATTCCAGCCAATGGCATCCGGCTGGGCAATGACTTCAGGTACAACAAGACTGTGACATACCAGTGTGTCCCCGGCTATGTGATGGAATCACACAGAGTGTCTGTGCTGAGCTGCACCAAGGACCGGACCTGGAACGGTACCAAGCCGGTTTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:58
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:
PF0008415=Sushi=WD(100=91.7)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.8)
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:
AACCCCGGAACTCCAAGCAAT
R:
CTTTGCAAACCGGCTTGG
Band lengths:
343-1468
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