MmuINT1007769 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128561791-128563417:+
Coord C1 exon
chr4:128561791-128561878
Coord A exon
chr4:128561879-128563278
Coord C2 exon
chr4:128563279-128563417
Length
1400 bp
Sequences
Splice sites
5' ss Seq
TTGGTAACT
5' ss Score
4.27
3' ss Seq
TATGCTCTGGCACTTTGCAGACC
3' ss Score
8.32
Exon sequences
Seq C1 exon
GTTTCCTCGGAGTCTTCTGGAGGCACCTTCGTCTACCAAGGCTCCGTCAAGGGCCAAGGCTTTGGGCAGTTCGGCTTTCAAAGACTTG
Seq A exon
GTAACTAGCAGTATGAGGGGGGGAGAGGGGTCTGGGGGGGAGGAGCTGTATCCTGGGGCAGGAAGGAAACTGATGAATTTTTTAAGTTCATCTGGGCCTGTATTACCTTAAGACTCAGACAGAAGCTGCAGTAGCTCCAAGAACAGATGCTAGACTGGCACTCAGCCTCGGGTTGCCATGCTGGCCACCGGGCACTACGGGCATCACCCCCGCCCAGAGGATCAGGGAGTTGCCGAAGTACCCCTGCATCAGGCTGCCCTTCCCTGTAACGTCATGGCTTCCTTAGCATTTCCCCAGAGAGCATGGAGTGCCCTTATGTCACAGACAAAAGACCCAAACGCTAAGGAACCTTATCCTGTTTGTCCTGTCCCAGGATTGGACTCCACACACTTGAGCATGACCACTCCAGAAACAGGTCCTGTCCCAGGGGCTCAGACTCACATGGAATAGGGTCCTAGCTTCTCAGGAACAACAAAGAAAAGATGGAGACAACCATGTGTCCCTGAAAGCCACCTCTGTATCCCACGTACCATGACCTCCCACTCCCAGGGCCCCTGCCTACCAGGCCATCCTCTACCTTCTCTGACAGCTCTCCCCTCCAGAAAGTTCTCTCTTCAGTCAGCTCAGATCTACTCGTGGCACCTCTTCCTCTCTACCCCTCCCCAAAGCCATCTCAGCTTTGCTCTCGAGGATCCCACATGTGGCAGTCCTCACAGCTCCTGACACAGACCCCGGACCCTCACTCCAGTAGTCGAAAGATCCCAGCAAACGTAGCCAACTCTCTGTTCCCTGTTGATCCCTAGCCCCTCAGCTAGGTGGCCCTTCACAGGGAGCCAATGGAGTGAGTGGCGAGCCTTCATATACCCCAACTCATTCCTGCCATGGCAATCCAACCTCACTGTGAGATATATATACATATATACATACACATATATACACATATACACATAAACATATATACATATATACACACACATACACATATATACCATGGCTCCACCTGATGAAAGCTTTCATCTAATAACAGGCTTTGATGGCCAAGAAAAGCGTAGAAACTTCAAAAGAACTTCATCCTTTGAAGGTTGTGTTCAGAGATATGACATCAGGTTCATCTGCTACCTATCTTCCATGGGACCTCCCCAACCCCAGCCCCCAGGGATAGCTGTGTTCCAGGCACAGTCCTCTGGATACAATGTGACCAGAGGCAAGCTCACATGGGCCTCCGGGGAGCTCTCTGAGAGCTTGTGAGGCAGGCAGCTGCTGTCTGGGCACAGGCTTCTGCCAGCTGAGCAAGAGCAGGTGACAGTACCTGCCGCTCTGCAGCAGGGTTGAGTGGCCAGTAGGGAATATCACCTCAGGGTGTGTCTGTGACTTGAGTGGTATGCTCTGGCACTTTGCAG
Seq C2 exon
ACCTCAGGCTGTTGGAGTCAGATCCCGAGTCCATCGGCCGGCACTTTGCTTCCAACAGCAGCTCAGTGGCCGCCGCCATCCTGGTGCCTTTCATCGCTCTCATCATCGCCGGCTTCGTCCTCTATCTCTACAAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:68
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:
NO
A:
NA
C2:
NO
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:
TTCCTCGGAGTCTTCTGGAGG
R:
TGTGCTTGTAGAGATAGAGGACGA
Band lengths:
224-1624
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