MmuINT0033369 @ mm9
Intron Retention
Gene
ENSMUSG00000000305 | Cdh4
Description
cadherin 4 [Source:MGI Symbol;Acc:MGI:99218]
Coordinates
chr2:179623794-179625681:+
Coord C1 exon
chr2:179623794-179624027
Coord A exon
chr2:179624028-179625447
Coord C2 exon
chr2:179625448-179625681
Length
1420 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
GTTGCTGTTCCTCACTCCAGGTG
3' ss Score
9.63
Exon sequences
Seq C1 exon
GGATCCCCCCAGCCAGTGGCACTGGGACCCTGCAGATCTACCTCATTGATATCAATGACAACGCACCACAGCTGCTACCCAAGGAGGCACAGATCTGCGAGAGGCCCGGCCTCAATGCCATCAACATCACTGCAGCCGACGCCGATATGGACCCCAACATTGGCCCCTATGTCTTTGAGTTGCCCTTCATCCCCACTACAGTGAGGAAGAATTGGACCATCACCCGCCTAAATG
Seq A exon
GTGAGCCCACCCAGCAGTGCCCTAGCCACAGGCAGAACCAGGAGCTAAGTATTTAGGGTCCAGCCCAGGATCTGTCACCAATGAATAGTAGCCATGGAGATGGGAGACAGTCCCCACCTCCTGGACTGTTCATACAGGCTGGGGAGACAGCCCTGTTTATCTGTGTCTCCACCACAAAGCTATTTATTTGTCCCTAGTACCTCCCTGTTCTAGAAAGAGCCTAGCTCGACCATGCTGGCAGCCATTACTGGTTGACTGGCCCCTGGAGACTACAGCCCTTGGGAGGCCCCTCTCCTGTATGGCCAGTGCTAGGAGCCTTACACAACCCTAGAGATGTAATGCCCATTTATGCTTCCACCAGCAAAACTGTCAATTCTTCAGGCCCTTGCCAACATGATAGGGTGTTGCTGCAGTAAGCAAAGCCACTGCTGTCCTCTGCCTCTGGGCTCCGGGCGGAGAACCTCCACATGCTCACTGAGGTTTGGGTTTTTGCTCAATGACTTTGCCTTTGTTCTTTGGGAGGGTTGGGGTTTTTTGGGGAGGGGGGTATTTGTTTGTTTTAAAGATCTATTTATTTTATGTATATGAGTACATTGTAGCTGTCTTCAGACATACCAGAAGAGGGCATCAGATCCTATGCTGGATGGTTGTGAGCCACCATGTGGCTGCTGGGAGTTGAACTCAGAACCTCTGGAAGAACAGTCAGTGCTCTTAGCAGCTGAGCCATCTCTCCAGCTGCCTGGCTCACTTTCAATTCTGATATGGTTGATTTTTTTTGGGGGGGAGGCTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAATGCTGAGATTAAAGGCGTGTGCCACCACCGCCCAGATGATGTTTTAACTTTGTGTGTCACTGTATGTGTGCAGGTGCACATATGTGCAAGTGTGTGTGTGTGTCTGCATGGCATGTTGTGATGTGTGTGCATATGTGTACATTGTGTGCATGATGTATATACATGTCTCTGTGTGTGTCTGTGTGTGTGTCCACATGTGTACATATGTGTGCATGATGTGTGTGCATGAACATCTGTATGGTATGTGTGAGGTGTGAGGTGTATGCATATGTGTACTTTGTGTGTGTGATGTATGTATATGCACATGTGTGTGTCTGTGTGAGACCACATGGTATATTGTGATGTGTGCATATGTGTACATTGTATATATGCTGTACATACATGCGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGTGGGGGGATTTTTCCTCTCAGTGCCTGCCTGTGGAAGTCTTCCTTGGGAAGGACAGCTGCCCATTGGCTGCATGTTGCTGTTCCTCACTCCAG
Seq C2 exon
GTGACTATGCCCAGCTCAGTCTGAGAATCCTGTATCTGGAAGCAGGGGTGTATGACGTCCCCATCATCGTCACAGACTCTGGCAACCCTCCCTTGTCCAATACATCTGTCATAAAGGTCAAGGTGTGCCCATGTGATGAGAACGGCGACTGTACCACGGTCGGCGCAGTGGCTGCAGCTGGCCTGGGCACGGGCGCCATCGTGGCGATCCTCATCTGCATCGTGATCCTGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000305-Cdh4:NM_009867:12
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=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.0),PF0002812=Cadherin=PU(54.3=64.6)
A:
NA
C2:
PF0002812=Cadherin=PD(44.7=53.2),PF060846=Cytomega_TRL10=PU(58.5=69.6),PF0200911=Rifin_STEVOR=PU(54.9=35.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGGACCCTGCAGATCTAC
R:
CGTTCTCATCACATGGGCACA
Band lengths:
358-1778
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: