MmuINT0033358 @ mm10
Intron Retention
Gene
ENSMUSG00000061048 | Cdh3
Description
cadherin 3 [Source:MGI Symbol;Acc:MGI:88356]
Coordinates
chr8:106552866-106557297:+
Coord C1 exon
chr8:106552866-106553012
Coord A exon
chr8:106553013-106555240
Coord C2 exon
chr8:106555241-106557297
Length
2228 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GCTGCTCTCTGCTTCCCTAGAAC
3' ss Score
9.02
Exon sequences
Seq C1 exon
GACTATGACATCACCCAACTCCACCGGGGACTGGAGGCCAGGCCTGAGGTGGTTCTCCGAAACGATGTAGTGCCAACCTTCATCCCCACCCCCATGTACCGACCCCGGCCCGCCAACCCAGATGAAATCGGGAACTTCATCATCGAG
Seq A exon
GTAAGGCATGGCAGGTTTACCAAACACAAGCATGGGTCAGGCACAACCATAGGAGAACAAACATGGGCTTTCTGCATAGACTGAGTTCTAGTCCCGGCTCTGCCCTCCAACTACTTGATCTCTGCATACTTGAGTATCTGTGGGTTTCTCTTTCCTCCTCCATAAACTCCAGGTTTAAACACTGAGTTACTAGCAAAATACTCTGGAGTCAGTCAGGCAACTTAGGTTTTATTTGGGGTTTTTGGTGTTTAAGATTCTCTCTCTCTCTCTCTCTCTCACTCACTCACTTACTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTGCCTACATTCATGTTTGTAAACAACATGTGTACAGTGCCCTCAGAGTCCCTGGGACTGGAGTTGGAGACAGTCATGAGATCCCAAGTGGGTGCTGGTGCCTGAAACCCTGTCCTGTGGAAGAGCAGCCAGTGCTCTTAGCTGCTGAGCCATTGCTCCAGCCTCGGCTTGCTTGGTTGGTTGGTTGGTTGGTTGATTGGTTGGTTGATTTGAAACAGGGTTTTTCTCTGTGTAGCCTTGGATGTTCTGGACCAGGGCTCTCTGTGTAGGTCAGGCTGACCTCAAACTCACAGAGACTCTCCTGCCTCTGCCTTCCGAGTAGTGCAGTTAAAGCCTTATGATACCATTCCTGGCCTCTTGGCTTTTTACTTTGTTTTTGTTTTATGTTTTGTTTTGTTTTTTTTTAAAGATTTATTTATTATATGTAAGTACACTCTAGCTGTCCTCAGATACTCCAGAAAAGGGCGTCAGATCTCGTTATGAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATGTGAACTCCGGACCTTTTTGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCTGTTTTTATGTTTTATTTATGTATTTAGTGTCTATCCCCCATATCTGCCATGGTACACATGCATTAAGAGTATTCGCTGCTCTTCTAGAGGACTGGGACAAAGATTTGAAACCTTCTAGAGGACAGGATTTGAAACCCTGTCTCAAATCAACCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCCCAGTCTGAAAACCCATACGGAGACCCACAGCTCTCTGTAATCCAGTTCGGTTCTAGGGGTGTCCAGTGCCCTCTTCTGGCCTCCACCGGCACTGCATACACATGGTGCATAGACATACGTGCAGACAAAACACCAGTGCACATAAAATAAATAAAGCTTTTAAAAATAAAAGTAACAAAAAAATTGAAATTAAAATAAAAATAATTTTTAGGCCTGGCTTGGTGGTATACACCTTTAATTCCAGAACTCAGAAGGCAGATGGATCCCTCTGTGTTGGCCTGGTCTACAGAGTGAATTCCAGGACAGCCAAGGCTATGTAGAGAAACCCTGTCTCAAGCCCCTCCACATAATAATAATAATAGTGATTTTATTTATTTATTTATTTATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCGTCAGATCTCGTTACGGATGGTTGTGAACCACCATGTGGTTGCTGGGATTTGAACTCCGGACCTTTGGAAGAGCAGTAGGGTGGTCTTACCCACTGAGCCATCTCACCAGCCCTATTTTTTTTCTTTAAGTTCAGTGTAGTAGTACATGTCTTTAGTCCCAGAATTTAGTAGGCAGAAGCAGGCAGATCTCTGTGAGTTCAACACCGGCCTGGCCCACAGAGCTCAGAACAGCGAGGACTACATAAGGAGACCCTGTCTCAAAAACAAACAAACAAAAAACCCACAAAGGTCTGGAGAGGTGGCTCAGCAGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGTTCATAACCATCTGTAATTGGATCCAATGCCCTCTTCTGGTGTGTCAGAAACAGTGACAATATACTCATTATACAATAAATAAATCTTTAAAAAACAAAAACAAAAGAATTTTAAAAATAATTACGTTTATGTGTCTAGGAAGAAAAATGTCGATGTGGAGATGTGGAGATGTGGAGGTGGGGGTGGGTATAGAGGCTCGGCAGGTGTACTGATTTGTCAAAACCCAGGTCGCTGGCAAGGGTCTCCATCCAATCAATGCTGACCGCTGCTCTCTGCTTCCCTAG
Seq C2 exon
AACCTGAAGGCTGCCAACACTGACCCTACTGCCCCGCCCTACGACTCCCTGCTGGTTTTTGACTACGAGGGCAGCGGCTCTGATGCCGCCTCCCTGAGCTCCCTCACCACCTCCGCCTCCGACCAGGATCAGGACTACAACTACCTTAACGAGTGGGGAAGTCGATTCAAGAAACTGGCGGACATGTATGGTGGCGGTGAGGATGACTAGGCTGTCCCTGCCAAGCTGTCCAGGCAAGAACTACAGACGGGTCACAGCAGCATCTCAAGGGAGCCTGGCTCCCGCTCCAGCCAGGACTCTGAAGTTTGCCCAGAAGTGGCCTGCGTGGCACGCTGCATCTGACCAGAAGGCTGGACTGTGAGCCTTTCCGATGGAAGGATGTGACTCTGACGACAACACTGATCCCCACCTCAGCCATGGCTGAGCCCCTCTCAGAGCGGGAATGTCTAAAGGTCTCCCGCCTGCCACACAGCACTCAGCTCTGCCCTCTCAGGGCTTGAACTTGCTCCGATGCCCTCGGTGACTTTCCCCACTTGGAATGGCTCCCTCTCTTTAGAAAGAGGCCCCTAACTAAGGCCCTGTTTTTCTTTAATGCAGTTTTCAAAAAGAGGCTGGGGTGGGTGGGGCAGGGTGCGGACATCAGTGTCCCCTCAGGCCCTCCAGAAGAGAAGCCTACAGGGCACTGGCCCTGGTACATTTCTCTGACATTTCTTGAGGCCTCACATTGGGGAGGGGTCACTGCCTTTTTTTTTTTTTTAATACTGAGTATATCTAAGTTGTCTCGTATTTTTTTATTTTCCCTGTTATGTGCTGTAGATGGAGAGTGATGACAATCGTGTAAATGTACTAGAATTTTTTTATTAAAATGAACTTTTTTTTTTCCCAGAGGTGCTAGGGGAGTGGATTTAAAAAGACTTTTTAACCTAGTTCTCAGAAGTGTTTGGCTTGGTGGGTTTTAGATTTTTTACAAGATTTGCAGACGCCCTCGCTTCCACCCAACTTCCCCCTTGTGGCTCAGGATTCAAGCTGATCTCAGGCCACAAAGGAGGAAATGATGGCATGACTGGCCGGAGGTGGGATACAGACTCCCCCCCCCCCCCCCCCCCCCCCCCCCGCAGCTTCAGAGCTATGAGAGCACCACAGTTAACTTCCTTCCCTGGAATTGATTGCTCCACGCCCATAGTTACAGGACTTGGGAGGTGAAATCAGGAGCTCAGAGTCTGGGCGTCAGGGGATGGGGGTTGGGGAAGGCTCATGGGTGATGGAGCTGTAATCCTAGCACACCACAGAGGCAGGAGAGCTCACATTGGAGGTCAGCCTGGGTTACCTATCACAACTCTGTCTCAGAGAACAGAAATACTTTCCAGGCCAGCCAGAGCTTTGTAGTGTCTCAAACAAACAGGTTTTCTGGTTGAGTATTGATAACCTGCCACGTGGTAAGGGCTACCGCTCACTCGGAACTTAGAAAGCCAGCAGCACTTAGCTTTGATGACGTCTTTCACTTGGCCTCACATCCATCCTCTGAGGAGGTTTTCCTACATTACAGAGTGACAGTGACTTCTTTGTGAGGGTTGGGGTTTTTTGGTTTGTTTGTTTTTGCTTTTGCTTTGTTTTTGTTTTGTTTTTGCTTTGTTTTAAATGATATGTAAAACAGAAAATTAGAGAATTCACTTAATTGAGTTGGTTATATTAAATTAGAACGTTCCTGACCATGCCCGGGCAAGAGAGCCTAAGACAGAATGATGTCTTTGAAGTGAAGCCCAAAATTTTTCTTTTGTTAACAATTTTCTATTGTTTTATGTATGTGGGTGTTTTCCCTGCATGGACATCTCTGTACCACGTGTATACCTGGTGCTCCTTTTGCCCAAGGAGGCAATAGAAGAAAGTGTTGGATCCCCGGACCTGGGTTATAGAGTGTTACAAGTTGCCCTATGGGTGCTGGAAATCAAACCCAGGTCCTCCTGAAGAGAAGTCAGCATTCTTTACCATTTAGCCATCTCTCTCCAGGCCCACAAAATTGTTCTTTTCAAAAAATACAGAGTATTTTTCAAGATTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061048:ENSMUST00000080797:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.333
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(32.0=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.3=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
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
- Pre-implantation embryo development
- 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