MmuINT0124881 @ mm9
Intron Retention
Gene
ENSMUSG00000039457 | Ppl
Description
periplakin [Source:MGI Symbol;Acc:MGI:1194898]
Coordinates
chr16:5102649-5104639:-
Coord C1 exon
chr16:5104544-5104639
Coord A exon
chr16:5102772-5104543
Coord C2 exon
chr16:5102649-5102771
Length
1772 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGT
5' ss Score
7.33
3' ss Seq
TGTCCTCTGATCTCCCTCAGTTT
3' ss Score
9.16
Exon sequences
Seq C1 exon
GCACACATGGAGGCTGTGCATGCTGAGTGGAAGGAGTACCTGAACCTGCTCATCTGTGAGGAGAGCCATCTGAAATACATGGAAGACTACCACCAA
Seq A exon
GTAGGTACCTGCCTGGCTCCAGGCACGTGATAGGATTCAGGAGTTCCTGGGTGCGCACAGAGCCCCACACATGCATCTGGAGGTCAGAGGACAACTTGTCATGAGTGAGTCTCTCCACCATGCATCAGGGGACTCAACTCAGGTCATTGTGCTAATGCCATGGGCACTTTTATCTGCTGAGAGATTTCACTAGCTCAAGGTTTTGAATTTCTGACGTAGGATCTCATGTAGCCCAGGCTAACCACTCTCTGTGTGAGAGAGGATGAACTCGACTCCCAATCCTCCTGCCTCTACTCCACCTTGGGTTTAATTTTGCTGAGATATAAAAAATATAAACTTTACTATTTAGCCCCCTTTTCAAGAAAACTAACATTCCTACCCTCACCCCCTTTTTTGAGACAAGTTCTCAATGTATAGTCCAGACTGTCGTTGCATTCAAACTCTCCACCATTCTCCTGTCTCGGCCTCTTGAGTAGCACCACCATGCCTAGCTCATTTTTACCACTGACCCATTTGTTACATTAACAATACAGGACAACCTCACCCTCTGTTTCCTGAACTTTCTCATCAGACAGATAGAAATTGAGTGCCCACCCCCAACACACACACACACACACACACACACACACACCCGCCTGATGACCTCTGACCTGCCTCTGGGTTTGCCTGGTATTAGCTAGCGTGAGCACAGGCAACCCAGAACGGTGCCTCTTGCCCTTGTGTGTCCAGCTCTTCTCACTAAGCATGATGGCCCGAGCACAGTGCAGCATGTTGCTATGTTTGTGTGCTTTTTATTCTTGTGGCCAGGTGGCTGCCTATTGTCCAGGTGGGCACCTGTTTACATTGCCATCTATTCATAGACAGTGTTTCCATGGGAAACAGTAGGAGCTGTAGGTAGTCGTCGTAATTCAGGGTCTTCCTCACACTTTCCCAGTTCTAGCAATCGAGCCCAGGGCTTCACATAGGCCAGGCCAGGCCCCACCTTTAAGCTGTATTCCCAGCATCCCTTTACCTTCTGTCGGAAGATGGTCTTACTAAGTGGCAAACTTGTACTTGTGATCCTCCTGCCTCAGCCTCCTGAGTGGCTAGGATGACAGTACTCACATGCCTGCTTGATCTAGAGTCTTCAGACTGGAACTTGAGCTCAGGGGGTACCTCATAACTCTTTCTGGAGTATCTGAGCAACACAGAATTTCACAAAGGTCCAAAAGTCCTCCTCAGAGCAGCAGCCCGAGCGTTCAGCCGAGGGGACAACTGAAAATAAATGAGTCAAGAGGTGGTGAACCAAAAGCTGGGCAAGGGAACTTTCCAAAACAAGAAGAGGAGGTAGCTAGCAAGGCTTAGAATTAAAGCATGGTTAGGTGCTGCTAAATGGTACAGCCGGCTTCTGAGAAATGCATTGCTGGGTGATTTTGTTACTGTACAAACCCATGAAGTACACTTACACTGGGTGGCTTCACAGGGTGAGATGCTCTTAAAGTCCCTGTCATCTGGAGGGGCCTCAGCTGAAGGTTTGCATACAGCCGCATTGTTAGGGTGTTCCTGGCACACAGAGAGAACGCCTGAACTTACTGGCATCTAAAGATATATAGAGGTGGGGTGTTGGGGATCCAGTTTTTCTCCACTGAGGCCCTGCACAGCCAGGCTGAAGTGGGAGTCAAAGAGGCTCAAGCAGGTCATATCATAGATTTAGGCCCACCTAGGGGATAAGCAGCCGTCGGGGTGTGCGTGGTAGCTTTCCATCTGTGATGGTGTCCTCTGATCTCCCTCAG
Seq C2 exon
TTTCACAAAGACATGAAGGATGCTCAGGAGCTGCTACGCAAGGTGGACTCAGACTTGAACCAGAAATATAGCCCTGACTTCAAAGACCGGTATCAGATAGAGCTGTTGCTTCGGGAACTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039457-Ppl:NM_008909:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.049
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(22.1=71.9),PF123293=TMF_DNA_bd=PD(2.8=3.1),PF0043516=Spectrin=PU(5.1=12.5)
A:
NA
C2:
PF0043516=Spectrin=FE(50.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACACATGGAGGCTGTGCAT
R:
ATCCAGTTCCCGAAGCAACAG
Band lengths:
218-1990
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: