MmuINT0033092 @ mm10
Intron Retention
Gene
ENSMUSG00000000303 | Cdh1
Description
cadherin 1 [Source:MGI Symbol;Acc:MGI:88354]
Coordinates
chr8:106666187-106670246:+
Coord C1 exon
chr8:106666187-106666330
Coord A exon
chr8:106666331-106668405
Coord C2 exon
chr8:106668406-106670246
Length
2075 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TACGGTGCTCTTCCTTTTAGAAC
3' ss Score
10
Exon sequences
Seq C1 exon
GACTTTGATTTGAGCCAGCTGCACAGGGGCCTGGATGCCCGACCGGAAGTGACTCGAAATGATGTGGCTCCCACCCTCATGAGCGTGCCCCAGTATCGTCCCCGTCCTGCCAATCCTGATGAAATTGGAAACTTCATCGATGAA
Seq A exon
GTAAGTAGACAAGGCTGTGAGGCAAATCACAGTACATCTCTTAACTCCGAACCAAGAAGAAAAGCGTTCTAAATGAGGAGAACCTTCCAGTGGTTGCTGTACTGTGCCTATGTCCCCGAGACAAAAGCAAAATCTACTTGCAGAGATTTAGGAGACCTAGGAGTTACAGAGCAAATCTGCTTTGCATGAGTTTCCTGCATTCATTACACCTGTTTGGGGGAGTGTCACAGGGAGCCAAAGGCCGCTTGGCAGGTAGATAAAACAGCATCTCAGCTACATGAGGACCGTAGTTGGTGCCTCAGATACACTGTAGTTGGCATCCGAGGCACCAACGTAAATGCCGAGCAGGCATGGTGGCCTGTTTATTCTAGTGTTCAGATTAGAGCATCCTGAATCAGCAAGCTCTAGGTTCTGTTGTCTGAGACCTTGTCTCAGTAAATGAGGTAAAGAAAAGTTGAGGAAGACCCCTGATATTGTCAACCTTGGGTTTTCATATGCACATGTGCACACAAAAACACGCTATACATAGCACACACAGTGTTTTCCAGATTACCTAAGGCCCCTAAAAATAGCATCCCTCATGTAACATACTCACGTAACGTACTTATATGTGTTAGAAATAGTTTCAGCTCTGATCAAAACACTTAAACAGATAATAGGAGATGCTGGGTTCAGCATTCTATTCTGTTGAAAACATATGCACATATATAACATATTAACTCTTCTACCATCCTGCTCCATTATTTTGCTGTCTTAGGTGTGTTTCTTTCTCCTCTTTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCCTCTTTTCTCTTCTCTTCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCTCTCCTCTCCTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCCAAGACAGGGTTTCTCCATGTAGCCACAGCTGTCCTGGAACTCTCTTCATAGACCAGGCTGGCTTCAATCTCAGAGCCCCACCTACCGCTGCATTCCCAAGTGCTGGGATTAAAGGTGTGGGCTGCCACTGCCCGGTATTGGTTACTTTTTTTTTTTTCTTTTTTGCTGTGCCAAGATACCATGCCTAAGGCAGTTTACAGAAGGAAGAGTCTAATTTGGGGTTCTAGAAGGTTAGAGTCCATGACAATCATGGCAGGGAGCCTGGCAGCGGGTAGACATGCACAGCTGGAGCAGGAGCTGGGGGCTCAGGCCAGCCTGGTCTGCAAAGTGAGTTCCAGACAGCCAGGGCTATACAGAGAAACCCTGTCTCAAAAGACAAAAACAAAAACCAAAAAAAACCCAAAAACCAACCAACCAAACAGAAAAATGTCAAGCCTTGGCCATGCCTTTAGTCCTTGCACTTGGGCGATAGTAGGTAGCAGGTGTATCTCTGAGTTTGAAGCCAACCTGATCTACAGGAGGGAGTTCCAGGATGTCCAGGAAAAACCTGGATTCAAAGAAAAGCAGAAAAAGACTGAAGCCTGTTCTCAGTAGCACACCTTCTCCAACAAGGCCACACCTCCTAATCCTTCCAAATTGTTCCAGCTGGGGACCAAGAGTTCAAACACTGGCTGGCTTTGTATGTACTCGCTATGTAGATCAGGCTGGTCTTGAAGTATGTAGCAGAGGAGGACTTTAAATTCCTGATTCCCCCAACTTCAGAATTAACATTTAACAATAGCAGTTTGTCATCTGTCCTTCGAGGATTTTCTGGGCTGAACTGTAACCTACGTGTTTTAGTATGACGACTCTCGTTGCTCTTACCCTCTGTCCAGCCTGGCCTTGGGACTTTGCCTTCTGTGCTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCTTGAAGGGGTTAACTACTCCTTGGTTAGTTTTTCATGTTTGGGGTGTTGCTTGCCTCTGATGCATACTGATAAGTACGGTGCTCTTCCTTTTAG
Seq C2 exon
AACCTGAAGGCAGCCGACAGCGACCCCACGGCACCCCCTTACGACTCTCTGTTGGTGTTCGATTACGAGGGCAGTGGTTCTGAAGCCGCTAGCCTGAGCTCACTGAACTCCTCTGAGTCGGATCAGGACCAGGACTACGATTATCTGAACGAGTGGGGCAACCGATTCAAGAAGCTGGCGGACATGTACGGCGGTGGTGAGGACGACTAGGGGACTAGCAAGTCTCCCCCGTGTGGCACCATGGGAGATGCAGAATAATTATATCAGTGGTCTTTCAGCTCCTTCCCTGAGTGTGTAGAAGAGAGACTGATCTGAGAAGTGTGCAGATTGCATAGTGGTCTCACTCTCCCTACTGGACTGTCTGTGTTAGGATGGTTTTCACTGATTGTTGAAATCTTTTTTTATTTTTTATTTTTACAGTGCTGAGATATAAACTGTGCCTTTTTTTGTTTGTTTGTTTCTGTTTTTGTTCTTTTGAGCTATGATCTGCCCCAGACACAACAGCCCCAAGCCCCTCACACCTCACTAATTTTTTACATTGTGTACTTGCCCTCAATTACCATGTTTGCTGTATTCTAATAGTCACTCATGTTCCTGAATTCTGTTGCCCTGCCCAGGTGATATTCTAGGATGCAGAAATGCCTGGGCCCTTTTATGGTGAGAGACAGGTATCTTGGTGTGGGTGCAACTGCGCTGGATAGTGTGTGTGTTCCCAAGATCTTTCGTGGTATTCCCTCTCCACCTCCAGAGAACTCATTTACAGTGGCATTCCTTGTTCGGCTATGTGTCTGGGGCAGAACAAAAAAAAGGGACCACTATGCATGCTGCACACGTCTCAGATTCTTAGGTACACACCTGATTCTTAGGTGCATGCCATAGTGGGATATGTTGCTTTGATCAGAACCTGCAGGGAGGTTTTCGGGCACCACTTAAGTTTCTTGGCGTTTCTTTCAAACCAAAACTAAAGAATGGTTGTTCTCTGAGAGAGACTGGAGTGCCACCACCAAAGACAGAGGAGAGAAAAGGAGAGAAACCAAACTTGGGGACAGCAACATCAGCGAACCCGGCTAGTTGGCACACCGATGGTGAGGGTACACAGGCGGTGAGACCTATCCCACAAGATTTCTGGAAGACTAGGCTTATCTCAACCAATGTTTTCTGGCTGGAATCTTTGTCCATGTATTCCTGAAGCCCAGGAAATGCACCCCTCCAATGCCTGCTCTTGATGGTAGCTACAGAAAATGCTGGCCGATTTAAACCCAAGTTGCCCAGTTCTGAGTAGAAAACTGAGACTATGCTGTGTGTGGCGGCGCGCACCTTTAAGCCCAGCACTCAGGAGGCAGAGGCAGTCAGATCTCCCTGAGTTCGAGGCCAACCTGGTATATATAGTATAGTAAGCGAATTCTAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCTGCAAACCAAAAGAGAAAACTGAGAATATTACAAATTGTGCATTTTCTCAGGAAGCAGGAAGAGAACATTCTAACGGGAAAAAGGAGACAAGACCTTTGAGAGTTTTCATTCAAAATGCAAATCTCAGCTTTTTGATAACCACTGGAAAGAATTTTATTGAAAGTTCTGTACTTACCTAACTTTGGAAGAAAATGATGACCACAATCAACTGTGAGAACTGTTGATTTCTCTGTAGTTTAATCATGTAATGTTGCTAGAGTGACCTTTGTATGTAGTTTGAGTGTATGTGTGTGGGTGCTGATAATTTTGTATTTTGTGGGGGGTGGAAAAGGTAAGCCATTGAAACCGTTCTCTAAGATGCATTTTTATGAATTTTATTAAAGAGTTTTGTTAAACTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000303:ENSMUST00000000312:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.771 A=NA C2=0.710
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(31.8=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.9=92.9)
Main Inclusion Isoform:
NA
Other Inclusion 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