MmuINT1006602 @ mm10
Intron Retention
Gene
ENSMUSG00000061048 | Cdh3
Description
cadherin 3 [Source:MGI Symbol;Acc:MGI:88356]
Coordinates
chr8:106510891-106511341:+
Coord C1 exon
chr8:106510891-106511006
Coord A exon
chr8:106511007-106511223
Coord C2 exon
chr8:106511224-106511341
Length
217 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CCTTCTACCCTCACACTCAGGTT
3' ss Score
7.97
Exon sequences
Seq C1 exon
AAAGCTGCACCCGGAGCTTAGCAGAGCGCGCCCCACCGTCGCGGCAGCCTTCTCACCTCCCTTCAGTTATGGAGCTTCTTAGTGGGCCTCACGCCTTCCTGCTCCTCCTGCTCCAG
Seq A exon
GTACCACAGTGCTTTGCCATGGTCCTGACCCGGATTGTTCCCTGGAGGGCGGGTGGGGTTCTCACGCTGCGGGCGTCGGGGGAATCTTAGGGCTGTGCTCCTTGGGGCCAAGGTTGTCCCGGAGGGCCCCCCCCCCAGGACTCCCAAGAATGGGTGTACAGAACCAGGCATGCCTGTGACTCAGCCTCCTCTTTAACCCTTCTACCCTCACACTCAG
Seq C2 exon
GTTTGCTGGCTACGCAGCGTGGTCTCCGAGCCCTACCGAGCGGGCTTCATCGGGGAGGCTGGAGTGACCTTGGAGGTGGAAGGAACTGACCTGGAGCCGAGCCAAGTTCTGGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061048:ENSMUST00000080797:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
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
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCCGGAGCTTAGCAGAG
R:
CTTTCCCCAGAACTTGGCTCG
Band lengths:
228-445
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