MmuINT0120903 @ mm9
Intron Retention
Gene
ENSMUSG00000041957 | Pkp2
Description
plakophilin 2 [Source:MGI Symbol;Acc:MGI:1914701]
Coordinates
chr16:16261697-16262831:+
Coord C1 exon
chr16:16261697-16261861
Coord A exon
chr16:16261862-16262657
Coord C2 exon
chr16:16262658-16262831
Length
796 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGA
5' ss Score
8.55
3' ss Seq
TTTACTCTGTGTGTACTTAGCAA
3' ss Score
6.65
Exon sequences
Seq C1 exon
GCCACAGAGAACTGTGTGTGCATTCTTCATAACCTCTCCTACCAGCTGGAGGCAGAGCTCCCAGAGAAATATTCCCAGAGTATCTACATGCAAAACCGGAATATCCAGACTAACAGTAACAAAAGTATTGGGTGTTTTGGCAGCCGAAGTAGGAAACTAAAAGAG
Seq A exon
GTATGATGGGAGATCTTTGAGAGACTGTGGGCTGTAGATGCGGACAAAGGAGCAGTGGAGCGGGAGGCTCTGATTCCTGCATTCATGTTGGCTACTGTTTCAGATTATTTTAGTTCTCACATTAGTCCTCCTATGAGGCTTCACCAGGAAGGAAACAGGAACAGAAAATCTCATGAGTTTTCCTACATTAATTCAGTGTTTGGGTGACAAGGATAAACTTCAGTCCCCACTTATCCGGCTCTGGATTTGTGCTGTTAGCTGTTAAGCCATGCTGCCCTGTGTCCTTTGTGGGCCATACTTCAGCCATTGTTTGAACATTACCTGTAGCCTAAAAATAAACCATGATAAACACATTAAGAACAAATTTCCTAGGAGGATGCATAGCTCTTTCAAAACTAACATAATAATGAAAAAAATGTTCTTAGTATTGTGGTATTCTTGAATTTGGAAAATGGCTGGTAAATTTAGACCCTTGATACTATTCCAAACCATTCTCTAAGCATCTGAGGAAACAGACATGTTTTTCTTGTCTTCAAAGTAATGGCAACTATTTAGAATTTAGGCTAAATGCACTGGAAACCATTTTAGAAGGACCTATATTTAATTCCCTTACTATGATGTGTAAAATTGGAGAATGTGAGTTTCTTAGAAAGCAACAATTATTGTGAGCTAAAGTTAAGTAATTGAATATACTGTTTCTGTGATTTGTTAGTCTCTGTAGAGTGTTTCTGGTCTGTTGGTGTGGGTGCAGAGTTATAGGCATCACTTGAAGTGCATTTACTCTGTGTGTACTTAG
Seq C2 exon
CAATACCAAGACTTGCAGATGCCAGAGGAAAGGAGCAATCCACATGGCATTGAGTGGCTGTGGCATTCCATTGTGATAAGGATGTATTTGTCCTTAATTGCCAAGAGTACCCGAAACTATACCCAAGAGGCATCACTTGGGGCTCTCCAGAACCTCACAGCAGGAGGCGGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041957-Pkp2:NM_026163:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.161
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0051418=Arm=WD(100=72.4)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CAGAGAACTGTGTGTGCATTCT
R:
TCCTGCTGTGAGGTTCTGGAG
Band lengths:
326-1122
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: