MmuINT1007772 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128564009-128567656:+
Coord C1 exon
chr4:128564009-128564224
Coord A exon
chr4:128564225-128565019
Coord C2 exon
chr4:128565020-128567656
Length
795 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
TGTGGTCTGTTGGTTCCCAGCTC
3' ss Score
7.92
Exon sequences
Seq C1 exon
GAGAAGACCCAAAGTCCCATTCAATGGCTATGCTGGCCACGAGAACACAAACGTGCGGGCCACATTTGAGAACCCCATGTATGACCGCAACATCCAGCCCACAGACATCATGAGCAACGAGGCGGAGTTCACAGTCAGCACGGTGTGTACTGCGGTATAGCCCCCAGGCCTGGCTGCAGCTGCCACCGCCACCGAGTGCCCCGCCGCCAGCAGCCG
Seq A exon
GTGAGATTCGGGGGCTGGAGAGGGTGGGAGACAGACCGGCTCTGCAGGGGACACAGTGACCTGTGTACACACTGCTCCTGCACACAGGGGCACCCCACCACCACAGGCATGGAGAGCTGGCCAGTAGCATTAGGACCCTCACTGCAGATGAGAAAACTGAATTTAAGCACGTGAACATTAACAAACTTGAACAAGGCCATGTATCTAAGAAGAGTGGGTCAGAATCCGAACTGCAATAGGAAAGCTGACCCACAAGGGAATCAAAGATATAACCCGAAAGAAGCCAGGCGGGTGTGGCAAACCACCCGTTGGGGAAGTAGAGAGAGGAGGAGGTGTCAGGAGCAAGATGGTGGCCAGACTAGTTGATATGTGAAGGGACCAGAATCAACATCTGGCCTCCACATACATACATGCATGCATGAGCACTGCACTTTGTGTTGCCTGTGCATATGCAAACATGCAGACACCACACACACATGCACAAGCATGCATGCACACATGTATGCACTTGTGCATGAACATGTGCACTGCACACACACTGACACACACACACACATGGGGGTTGGTGGGTAATTAATGCTCTGCCACTGTGCACACTCCCTACATGTTCCCATCCCCAGTTGGAGAAGACTAAAATCCAAAAGCGAAAGACAGAACCAACTGATGCCCTTCTGTTCTTTCCTCCTGCTTGGCTTTGCCTCTTTGCCACCCCTCACCCTTCCACTCCTGTTCCCACCCCCACCTCACCCCTCCTTCCTCTCTTCCACCTACCTGCTGTGGTCTGTTGGTTCCCAG
Seq C2 exon
CTCCCCCCAGGGGGCAGGAAGGAGCTCCCCTGAGCACAGCGCCCAGTGCCCATCTTCGTCTGTCCCTCCGCCTACGTCTGCCACTGCTGGGCCTCGGGCCCTTGCCTGCCCTGCCTCCATCTGTGCTCGTCACCCTGGAGAGGACTCCACGATGCCCTGCGTTGGGCAGCAGAGGAAGAGGGCTGCAGCTGGAGGGAGGCAGATGGATGCAGACAGCAGAGTGAATGATGGGTGTGCACCTGAGCGCACACAGCCTCTCCTTCACTGTGTCCTACAGAAGAGACCACAGAGGCTTAAGAAAGGGAAGCGTGTGTATGCGTGTGCGTGGGTGCATGGGTGGGTGGGTGTGTGTATTGCGTGTGTGTGTGTGTGTGAAAGATGCCCTAGACACTGTCCCCACAAACCCAGAGGAGATGATGAGAAAAGCATCATTGCCTCTCAAACCAATGTGTCCCCATGTGTAGGGACATGAAGAATGAGTAAGAAGGTCACATCTCATGGGAGGTAGCATGCAGAAGCCACCTGGCTGCAGGGGTGGCCCCATTTGCACATCGATAGCAAGGATTACCTGGAAGAAAAGGGGGGACGTTCTTCAGATATAATTAGGTAATCAATGCAATTGTTTTTTTAACCATAATGACACTGAGTTCTAAGCCCAGTGAGTTAAGAAGTTATTTGGGGTCCTGGGCATCTTTGGAAACGAAGGGTAAAGTCATGGTGGAGTGGGGGATACAGCAGGAATCTGACTCAGGAGCCTGGCATCACCTCTGACTGTCAGCTGACCACAAGAAGAGAAAAAGACCTCTACAGACCAGACAGCACACCCTGGAGAGGACAGGAGCAAACCAGCCCTGGCTCCCAAAAGGTGGCAGCCACCGCTTGCTGACTTATTCTCCGTGCCTGACTCTTTATGTGTCACTTCTAGTTCTTCAAACACCACCAAAGCAGGACTCGCTGTTTCCATTCAGGGGTCAGGGAAGATGGACGCATGAGCCACAAAATACGCAGGAGGTGTAGGTGTAAACGCGAATCTCTCTGACCCTGATGTCCGCTGCACCTGCTACCAGAATACCCAGGTCTACAGTGGGCACCAAAGGCAGGAAGGGAGGGGAGTCTCAACAAGAAGATGTGTGTGTCTAATCTGGATGCTGCCGTCTGTGCCTGGGCAGCACCAGATGAAGCACCCAGTGCCCCAGCCTCCTGAATTGGTGCTCGCCTCTTGGCTTCCAACAGCCCGCAACCACAGCAGAGGACCTGGCAGCTCCTTAATCAAGAGAACGGAGCAAAAATCCCATTCTCTCCAGCTCCTGGCGGGTGTCTCAGAGTCATTTAGGCCAGTGTTTCTCAACCTGTGGATCACGACCCCTTTGTGGGTCAAGTGTCCCTTTCACAGGCCTAAGACCATCCTGCATATCAGATATTTACATTATAATTCATAACAGTAGCAAAATTACAGTTATGAAAAGGCAACAAAAAATTTTATGTTGGGGGGTCACCATCACGTGAGGAACTGTATTAAAGGGCGGCAGCGACAGGAAGGTTGAGAACCACTGAATTAGACAATGTCACTGTGTTTAGGTCATTAATGAATTCCTTATGAGTGTGGTCGGGAAGCTCGTGAGTTTAGAAATCAACATAATAACATTTAGATTCACCTTTCCCGTGTCTTACGGAAGGTCCCCATGAGCATACACCCCTGCTTCTGTGTGAACCGCAGTCTCCGACGCTTGTAGGACATATTGAAATAACAAATAGAATGTGTGTGGGGATGGACGGGGAGAGCCATGCAGTTCACAGGAACAATTAAAAGAGCTCGATGATGGACGGGCTGAAGTGAGGGGGTCTCCATTTCCAGCAGGAGCATCAAAGACCACAAGGGCAGGCCCACTCCTGCCCACACACCCTCTGGCCCTCTGGGACTTAGCATCCCTGCATCGGGTGGGAGAGGACCAGTCTAGACAAACTTGTTCATGCCCATTCTGCCCTTGATGGTGAATGCAGGAGGTTTTCGGGCTCCTTCCCCCCTCCTCCCCAGAGCTAGTCCAGTCTGCTCACCCAGCCCTGCCTCCTCCCCTCCCACTGTGTGTGCTTGGGAGGTCCCAGGAGACACTCAAGGAGCAAAGGCTGGTGGGCACCCAGCATCTGCTGTGTGTTACCCTCTCTCTGGCTTTGGGCACTTTTTCTTCATCCCCAGAGGCTCAGAAGAGAACTAGGCAGATTAAGCCCTTCACCCACCATCCCTGTATCTACCACCTCCATCCCACGAGGAAAAAAAAAAAGTAAAACAAAAACAAAAAAAAAATCTTTTGTACAGAGATATATTTTTATTATACAAAGTTTGTACAGTACCAAAAAAAGACAGGAAAAAAAGGTGTACATTTTTTTTCATTATTGTAGGTAAATGGTGTGGGAGCCTTTTTTGTAAATGTAATAAAATGTATAAATATGGTTTTCAGAAAGCATCCCTGCTGTAAATATGTAATCTACACCCCTTCTCGGCTTGTCTGCAGTCTGTGCATTTAATTTATCTCTCCCTGTATATGAGGCTTCCCCTAGGGTTCTGCGTTATGGGACTTTCCGGAATTTGAAAGCAATTTTAAATTTTTTGAATTCAAATAAAATATAAATTTTTGCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:70
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTGTGTACTGCGGTATAGC
R:
ACAGTGAAGGAGAGGCTGTGT
Band lengths:
344-1139
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