MmuINT1007725 @ mm10
Intron Retention
Gene
ENSMUSG00000028804 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:MGI Symbol;Acc:MGI:2386401]
Coordinates
chr4:128452411-128456928:+
Coord C1 exon
chr4:128452411-128452549
Coord A exon
chr4:128452550-128456740
Coord C2 exon
chr4:128456741-128456928
Length
4191 bp
Sequences
Splice sites
5' ss Seq
CACGTATGT
5' ss Score
7.26
3' ss Seq
GGGCTTTTTTTGTTCTCCAGATT
3' ss Score
8.52
Exon sequences
Seq C1 exon
CTCCTTGTGGGGGAGACCTAACCGGGCCATCAGGAGTCATTCTGTCACCAAACTACCCAGAACCCTACCCACCAGGCAAGGAGTGTGACTGGAAAGTGACCGTCTCTCCAGACTACGTCATCGCCCTGGTATTTAACAC
Seq A exon
GTATGTACCTTTCCCGGGCTGGGACACCAAGGGGTTTGAGACCTCCGGGATTGAGGACCTGGGTGGCCAGGCTAGTCCTCACAGGTGTGTGGCAGAGTTCTCAGGTCCAAGGGTAAGAGAGTCAGAGATGAGGGGTGGGGCTCCAGCATCCACTGAATGTCTTCTCTGCCCCGGGACCTGTGTCTGCAGGATTCTTGCAATAGTTTCCAAAGCAGCTAACACTCTTTCTCTTACACTTTTGCGGCTGCTAAACACAAAGGAGCCCTAACCTGGGTCTCCATGTCCTAACACATTGGCTGGCCCTTTCCCCAGTGCCTCCCTCCATCCTGAAGCTTTGCAGGTCTCCGTGACCTTTCCACCTAACCCGTGCACTCACACCTTCATTCCATTCCCAGGCAGTTCTCCATAGATCTGCCCTATCCCTTCCCTGCTTCCTCCCTCCAGTGGCCTTCCGGACTACTTAAGCCTGGCTACTACCCCAACAGACCCATTAGGAACTTTTCTGATAAAAGACTCCAGCATGGGCTGGGGAGGTGACTCAGTCAGTGTTTGCCACACAAGTCTAAGTCTCTCAACTTAAAAGGTCAGGCACGGTGACACATGGTTGTAATCCCAGCACTGGGGAGGCAGAGATAGGCAGCTAGCTCCCTGAGGCTCCCAGCCTAGCCTACTTGGCAAGCTCCAGGCTAGTGATGAAATTCTCTCTCAACACACAAAGTGAATAGCTCTTGAAGGAACAATGTCCAAAGGTGACCACTGTATGGTGTATGGTATAGGTGACCACTGAATAGTACGTATGTACACATGACAGCAAATTCCCACATCTCCATCTTCATGCTACTACCTCCTGCCTCGACTTGACCATTTATCATCTTCCATCCCAACGATGTCTTGGTCTTCACACTGGCTACTCTGTCTCGTCTAGCCTTCCAGGGCACTCTCTCTTATGGGCAACTTAATAACAAAGAAGCAAACAGGCAGCCTCTTTGTTTGTTTGTTTGTTTGTTTGTTTATCCCTTAATAAATCTACCCTCTTTGTAAGTGAGTTTTGAATTTCTGAGTTCGGTTTCTACAGTCTGATGCACATCCATCTGTCCAAGCAGGCCCAGAGCTCCAGTCAAACTGAATGCCTGGTGGTTTCCTGAGTCTCAAAGCCTCGTTCATGCCTATCTCACATCTGCTTCCCAGTGACTTTCTTGTTTCCCGTCCTTGTCCCACTGCTGTGGGTCATCTCAGTCCCTGGGATAAGCTCAGGCTGGACCACCATGGAAGAATGAGTGTGTCCCTCCCTGGAGACTGACCATTTTATAGACCCTATGTTATATACTATTGACCATTCTATGCAGTCAGGAGCATGACCTACGGTAGCCATGTTGTTTGCTCTGAAGGAGTTACTTTATTAAGTGTGCATCAAGCCAAAGTAAAAGAATGACTAAGGAGTGAGAGAGCAAACTGTGATCAAGGCAGGTGCTCAAAGCAGCCAGCAGATGTCAATGGGGAAGCCCATTTAGGGCAGGCAGCTGGAGTTGCAAGTGGAGCCTGCCCCAGGCAGAACAGAGCAGCAGCCCTTCTGCTGAGATATTCAAGTGAAAGAAGAAATAGCAACAGATAGAGATAACATCTTCCAATCAGACACCCACAACATCATACAAAAACCAACTGAGGAAGCTGAGGCAGCAGGAGGTACCAAGTGAGCTGTGCTCCATAAGTGGGCATTCCATGGCTGAACTTGGTATGGATAGACTTTTGACTTCTCTTTCCCACTGTAGGTACTCTTATATAACTGGATAAACAACAGTAACATCTGTTGAGCATTTCACCTTGAGAACAGCTAGGTAGTCTCAAGGACACAGAATTCTCACTCCCAGGATCTTCACTGTTTTGCCCTCCCTCCCAGTTAGGAGGAAGCCCACTCATTCCTGGAAGGGACTTAAAGGACACTTGGAGGCACACCTGCTTGGATCTGAAAGGTGGGAGGTGGAGATGCAGCCCCACTTTGAGAGTCAGCTTCTCAGTGGGCTCAAACAGCTAATAACAATCTACCAGCATAGTACCCATTACATTAGCAGAGCATCCACTGCTTCCAGCACCAGCTAGTTCAGGAAGGCAAGGCATGTGTCTAGCATGCCCTTTGTCCTTGGCACCAGACATGGTGCTGGGCATCTTGAAAGGGCTCAGATAAAAATCCAGTGATGTGAATAAGGTAGGAAGAGATACAGGCAGAAAAATGCTGGTTCCACCAGGATATGGTGGCTCATGCCTGCATGCCCAGCGCTGAAGCAGGATAGCAAAGAGTTCAAGAGCCCCAGGCCATCCTAGGCAGCAATGTGAAACTGTCTCAAAAGTGAGATGGATGAATGGATGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAGAGAGAGGGGGAGGGAGGGAGGGAGGGAGGGAGGGAGAGAGAGGGGGGAGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAAGGAAGGAAGGAAGGAAGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAGGTCATTCCACAATCTGTGACCAAGACAAACTCAGCCAGAGCCTTTCTCTGAGGACTTTTGAAAGAATGGGTAGTTTCCAGAATAAGGAAACTATGTCACTCAGAAAAAGGAAGCAGCCCTGTAGCCAACACTAGTATGGGAAGACTCTATGTACAGAGGACACACATCTGCTTTCTAGACACCCACTCTGTCTCCCTACTCACATTACCTTCTTTGCCACTACTCTAGCCAGGTTATAACCCTTCTCTGCACCATGTGTCTTGGCTAAAGGGTAGAAGAGCCACTTCATTCTCAGTTTAACTGAATGGTCCATCTCTGTGTCCCTGCCCATTCCAGGGCACGAGCGCCTTCGCATCAGAAATCTGTTTTCTGAAAGTACATTTACTTGTCAGCCCTCTCATCTCTTTACACTTGATTTAGTAAAAATTGCCTTCATTGGACACATGCTTAAGAGCAAAATCATGCATCAGAGAGCAGGCCGACATTAAGAGTTATCAGATACATACCACGCAGAGTTTCAAAAGGGTGAGCCAGCTAACACACACACACAGACACACAGACACACACAGACACAGACACAGACACAGACACACACACACACACACACACACACACACACACACAGGGCATGAGGGCTGCTGATACTCCACTTCTTCCTATCTGTCATTTTCCGTTACATTCTTTCTAGGCTGGTGTGTCCATCCTGCAGCCTATGAGCCTTATGTGTCCCATGATAGCTATGACTGTAGCCTGACATATTTGCAGATGACAACATTATGTCACAATATCAAAAGCTTGGATGCCCCTGCTAGCTGCCCTACAGGGATAGATTATATCCATGAACTCCTGTTCTCAGTTAGGATGGATTTTCATCCCACACTAGGATCAGGTAGCTCAGGGAGAGACACCTGAAGGTGATGCTAGAACCCAGGTGGTGGCAGATGCTGAAGAGGGCCATGGCTGACATGTGATGGAAAGAGAAAACTAGGCTTTTCATGGTGGCAGGTCCCATACTTCTGGCGATGACTCCCTGGACAATTCTGTGCTCTTAGGAAAATTCAGTACAAACTGGTGTGATAGCAGAACAATGAAGTCAGGCAAGAGCCCTGGACTCACGCCTGCCAGCTTCACCCCTTCATGCCTGGAGTTGGCAACTTGCTTTCCCTCCTCCGTGAGCAAAACCCGAGGCCTTTGGCTACAGAACCAAGAACACTCAGCGACTAGAATCTTACACCTGTGTCCCCAAGCAACATTTTATACCATCTCTCCCGACCATGAGCAAAACCTGAGGCCTTTGGCTACAAAACCAAGAACACTCAGTGACTAGAATCTTACACCTGTGTCCCCAAGCCACAATTTGTACCATTTCTCCCGACTGGGATGTCACCTCATTCTCTTCAGTCTTTGGAGGGAGGGTGCTATGGGATGGTGGGCTTGCTTTCTGGGAGGCTCCAGCACAAACAAACCCCTGTTTGACCTCCATGGGGGGGGTGGGGATGGGCTTTTTTTGTTCTCCAG
Seq C2 exon
ATTTAACTTGGAGCCTGGCTATGATTTTCTTCACATCTACGATGGAAGGGACTCTCTGAGCCCTCTCATAGGAAGCTTCTATGGCTCACAGCTCCCCAGCCGCATTGAAAGCAGCAGCAACAGCCTCTTCCTCGCCTTCCGCAGCGACGCATCTGTGAGCAATGCTGGCTTCGTTATTGACTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028804:ENSMUST00000184063:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(41.5=93.6)
A:
NA
C2:
PF0043115=CUB=PD(57.5=95.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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