MmuINT0033090 @ mm9
Intron Retention
Gene
ENSMUSG00000000303 | Cdh1
Description
cadherin 1 [Source:MGI Symbol;Acc:MGI:88354]
Coordinates
chr8:109188096-109189424:+
Coord C1 exon
chr8:109188096-109188323
Coord A exon
chr8:109188324-109189293
Coord C2 exon
chr8:109189294-109189424
Length
970 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
CCTTCCTTCCTTGTCTCCAGTTC
3' ss Score
10.28
Exon sequences
Seq C1 exon
CTCAAGAATCTCTCATTTTGCAACCAAGAAAGGACTTAGAGATTGGCGAATACAAAATCCATCTCAAGCTCGCGGATAACCAGAACAAAGACCAGGTGACCACGTTGGACGTCCATGTGTGTGACTGTGAAGGGACGGTCAACAACTGCATGAAGGCGGGAATCGTGGCAGCAGGATTGCAAGTTCCTGCCATCCTCGGAATCCTTGGAGGGATCCTCGCCCTGCTGA
Seq A exon
GTAAGTTCAGGTGGCAGGTGCTTCAGCCCGTGACCTCTAAAACCAGGAAGGGCCATCTCCTAGGAGGAGCTTTTATTTGGGGTACAGGGGGCGCAGGATCCTTCTGTTCTGTCTGTCTCTGCTCGCCTAGATTGAGTGCATGTCCTTCAGTAAGTGGGGCTTCAGACCCAGGATCCCTGATGAGGCTCCTCAGATGCTTCATTTTAAACCAGTCCCCAAGGAATGCTGTGCTGGCAGAGCCAGGTTTACGTATAGCTCGCTGTACTCGTTAGCACAGGCAAGGCTGGCAGCTACCATCACCTCCGCATTCCATCTTGGAGGGCAGATGAGAGGGGAAGTAGAGGCTGCCTACCTGCAGGTTGTAGATGTCAGCAGCACTCACATCTCATTGGCCCAAGTGTAGCCATGACAAATGACAAGGCATCCTGGAAGCTCCTGCTCTTAGCTGGGTGATGATGAGCCCATTTTCATTGCATGCTTGGGAGACAGTGGTATTGGATGGAGGGCTGAGTGAGCAGCGGATGGTGCCCATGGCTGAAAAGATGAAGGAGAGTGGAGATGCTTGGAGGGAATCTGTCATTTTTGTCCGTGGTCTTTGTTCTGATTTTACCTGTCCTGGGCTTGGTAAAATGCCATGAGGATTTCAATGATCAAAGATACGGGGTTTTGCTTATTGAGGATATACCTTGACTTTTTTTGTCGGGGGCAGTAGATAAAGCTGGGGAAATTCTCTTATTAGACATTGGAAGCAGAAGTGGTATCAGGAGCCAGATGTCAAACTTGTTTATCATTTTTGTTATATTGTTTTTTGAGAAATGATCTCATTTGGCTGGACATGAGATAGTCCTCGTTCAGGTGGCTACCCACCTGCCTGGTGGGGTGAGGCTGTGGCATTCCAGGACAGTGGCTTCCCCTGGTCTTTCCTGCGTGTGGCTCATCACTCTTCCCTGCCTTCCTTCCTTGTCTCCAG
Seq C2 exon
TTCTGATCCTGCTGCTCCTACTGTTTCTACGGAGGAGAACGGTGGTCAAAGAGCCCCTGCTGCCACCAGATGATGATACCCGGGACAATGTGTATTACTATGATGAAGAAGGAGGTGGAGAAGAAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000303-Cdh1:NM_009864:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.364
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(44.9=51.9)
A:
NA
C2:
PF0104912=Cadherin_C=PU(22.3=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATTTTGCAACCAAGAAAGGACT
R:
TGGTCTTCTTCTCCACCTCCT
Band lengths:
346-1316
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: