MmuINT0033088 @ mm10
Intron Retention
Gene
ENSMUSG00000000303 | Cdh1
Description
cadherin 1 [Source:MGI Symbol;Acc:MGI:88354]
Coordinates
chr8:106661885-106663971:+
Coord C1 exon
chr8:106661885-106662030
Coord A exon
chr8:106662031-106663746
Coord C2 exon
chr8:106663747-106663971
Length
1716 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGG
5' ss Score
6.63
3' ss Seq
CCTTTTATGTTTTCTCATAGGTT
3' ss Score
11.18
Exon sequences
Seq C1 exon
GTATCGGATTTGGAGGGACACTGCCAACTGGCTGGAGATTAACCCAGAGACTGGTGCCATTTTCACGCGCGCTGAGATGGACAGAGAAGACGCTGAGCATGTGAAGAACAGCACATATGTAGCTCTCATCATCGCCACAGATGATG
Seq A exon
GTATGGACACCGTGTGGTCCCATCCCCATTGTGGCCTGGGCTCCATCCTTCTCCAGCTTGCTTGCCCCCTCTGCCTCTGCCTTACTAGGAGGAGGAGACTTCATTCTTTCTTTTATCTGTAACAAACAAACAATCAATCATAACATAAAACTTTTGGTAACTGAATTCCAAACTTTAGATCAAGTAGACTTTCTTTCCCTCTTCTCCCTTTCTGCACTTGAATCTCACTCCTTCCTGCAGGAACTTGGTTCATGGTTATGAACTTACTATTACTTAAATCTTATAATTCTTCAATTTATAATCTTATAATCTTCAACTTTTCTCTCTTTTATTTTGAATTTTATGTGTTTCTTAGGGTTTCATTTCTGTGAAGAGACACCATAACCAAGGCAACTCTTTTTTTTTTTTTTTTTAAAGATTTATTTATTATTTATTTTATATATATAACTATACTGTAGCTGTCTTCAGATGCACCAGAAAAGGCCATCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTAGAAGAGTTGTCAGTGCTCTTAACCACTAAGCCATCTCTCCAGCCCCCAAGGCAACTCTTACAAAGGAAAACATTTGGGGCTGGCTAAAAGTTTCAGAGGTTTAGTCCATTATCGTCACGGCAGGAAGCCGAGAGGCATGTGGGCAGTGGTGCTAGAGAAGGAGCTGAGAGTTGTACATCTTGATCCAAGGGCAGCTAGGAAGAGGCTCTGATTGAGCCTAGGCTGGTGGAGCCTAGGCACGGGAGACCTCAAAGCTTACCCCCACAGTTACACACATCCTCCCACAAGACCACACCAACTTGATTAAGGCCACACCTCCTAATAGTGCCCCTTTTTGTAGGGCAAGCATTCAAACACACGAGCCTGTGGGGGCCAAACATACTACCACAATGTGTATGGGTATTATAGCCTGCCTGTGTTCCTGGTATCCACAGAGGATGGTCACCTGGAACTGGAGTTACAGACAGTCAGGAGCTACTATGAAAGTGCTAAAAACCGAACCCTAAGCATTCTTAGTCACTGAGCTGTCTCTTCGGCCCCTTTTCCTTTCTGTATGGAAATGGGAACTGACCACAGTGCTAAACATAGACGTGTGTTCTCTACTACTTATATATATATATATACCACGTGGATACCCCAAGATTTTTTAGTATAGTTTAGTTTGTTTGTTTTGTTTGTTTTTGTTTTAGACATTGTTTCCTATATAACCCAGGCTAGTTTTGAACTCACGATGTAGCCCAAAAGACCTCAAAATTGATGTGCCCCCCCCCCCCATCCTGTGTGTTTCTAAGATTCCAACAAATTCTACTGCATTCTGCTTTTCCTAACCTCCTAATAAGATCTGCCGGAGCCAGGCTTCTGTAGGAGGTTGGGGTGGGATAAGGCTTTGTCTCAACAAACAAATGACAACAACAAAAAAAATAAACTCCCGAATTGGACTGTATTAGTAATGTACTAGAAAGAGAAGAAGAAGAAAGCTGCCTTTGAAATGAGAAATAATCTAAGACATTGTATACAGAGCATGCTTGTCAGAAAGCCGAGACAAGGACAGAGCGCCTGTGGTTAGTGTGGAACCTGCTGAGGGGTCGTGGACAAACTAAGAATTTGACCTCCTGGAAGGTGACACGATCCTTAATCTGTGACACCTTTTATGTTTTCTCATAG
Seq C2 exon
GTTCACCCATTGCCACTGGCACGGGCACTCTTCTCCTGGTCCTGTTAGACGTCAATGACAACGCTCCCATCCCAGAACCTCGAAACATGCAGTTCTGCCAGAGGAACCCACAGCCTCATATCATCACCATCTTGGATCCAGACCTTCCCCCCAACACGTCCCCCTTTACTGCTGAGCTAACCCATGGGGCCAGCGTCAACTGGACCATTGAGTATAATGACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000303:ENSMUST00000000312:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.180 A=NA C2=0.224
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=FE(51.0=100)
A:
NA
C2:
PF0002812=Cadherin=PD(15.6=19.7),PF0002812=Cadherin=PU(53.9=63.2)
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:
ATTTGGAGGGACACTGCCAAC
R:
ACTCAATGGTCCAGTTGACGC
Band lengths:
352-2068
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