MmuINT0120936 @ mm10
Intron Retention
Gene
ENSMUSG00000026991 | Pkp4
Description
plakophilin 4 [Source:MGI Symbol;Acc:MGI:109281]
Coordinates
chr2:59310102-59311913:+
Coord C1 exon
chr2:59310102-59310290
Coord A exon
chr2:59310291-59311693
Coord C2 exon
chr2:59311694-59311913
Length
1403 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CCCAAACGTTGATTTTGCAGTAG
3' ss Score
4.19
Exon sequences
Seq C1 exon
GCTTACGGAGTTCCTATGCCAGTCAGCATAGTCAGCTTGGGCAAGAGCTCCGTTCAGCTGTGTCTCCTGACTTGCACATCACTCCTATCTATGAAGGGAGGACCTACTACAGTCCAGTGTACCGCAGCCCAAACCACGGGACCGTGGAGCTCCAGGGGTCACAGACAGCATTGTATCGCACAGGCTCAG
Seq A exon
GTGGGCCCCATGTCCTGCTTCCCTCATCTCCTTGGCCCAACAGGAAAGAGATTTTATTAAGAATGGGTTCTCCATTAGAAGAAAATCGTGTCGCACCTTTAGTTGTCAGATAAGCAGCTGTGACAGCAAATCACAAACGGTAAAACAGAAGTTCGTTTAGCACATACTTAGGGGTAAAATATTTTTAAAATAGTGTAATCCAATGAAGGTAGGAATTATGCTGTTAGTTTAGGGACACATTTGTAAAACTGTAAATATGATCCCCTCAAATTAGCCTTATATCATGTAGAGAAAGGCAACCATTTGCTGAAATACTTCTGTGTGATTTTCGTTGCCAGAAGCAAGTTTTGAAATGATCCAGATGAGGGACTTGCTGTCGGTTAGCAGACCTGGAGGTGAAGACCACTCCACGTCACTCTTTTTCAGTGTGGGATTTCCTGTGAGAGACTCACACCAGGAGAGAGTGCAGTCAGAGTGTGTTTAATAAACAGGGTGCTGAGCCTCGCACCCAGTCCTCACCTTTTTTCTTACACCTCGGGTTCTGCTAGATCTGAAGCCAGAAACTGTACATTTGTGGTATCCATTGCCAGAGGTGCTGCAAGATGGCTTGAGAGGTCTCAAAGGTAGCTTCTAGCATTCAGGAAACCCTAAATCTTACAGTATGACCACTGAAGCCCGGTCAGCAGTGACAGCCCTCCCAGGCACGTCTCTAGAGGAGAGAAGACTGTATTGTTTCTTTACTAGAGATGGACAGTTCTGCCCACTGAAGGGTCTCAGTGAAGGGAGGTTCCTATGTTCTGACTATTGGCGGGAATTCCTCTAAGAGGACTGATTGCAGAAAGACTCCTGAGACCAGCAGTGAGAGATGCGCCTCCTTTCTTAGGAGAGAAGTATTCAGTGCAGCACACAGCTGCTTTGTACATCAGATCATTTAATAATTTCTGGAAAAAGCCATAGAATTTAAATCTATCTTTCTTGTGACATAGATTTTTTTTCCAATATTACCAAGATCCACAGATATAGAAGGAAAGAAACAGAACATTTAAAAGCTTGAAGGGTTATTTATAAATTTCAGCAAAAACCTTGTTTTTAATCACTAAATTAGAATTAAGAAATGATACCATTTTTTTTTCTGAGATTAATGTCTTGTAATTTTACTGAGATTTTAATTTCCTAAATCTTAATGTAGCCAAGCCCATAAGCAGACTCCTGGCTTCATTGGCTTTCTTTTCTGGGTGCCTCATTTAGTTCTTAAGCTAGGTTTATGAAATCCAAAAATAAACAGCCAATGCAATTGCCAAATGTTTAATCCTATTTAAAAGTAAAAATATATATATTGTATGTTTGAAAAGTGCGACTCTGTGAAGAACATACTAACCTTTCCCCAAACGTTGATTTTGCAG
Seq C2 exon
TAGGTATTGGAAATCTACAAAGGACATCCAGCCAGCGAAGCACCCTTACATACCAAAGAAATAACTATGCCCTGAACACAGCAGCTACCTATGCGGAGCCCTACAGGCCAGTTCAGTACCGAGTCCAAGAGTGCAGCTATAACAGGCTGCAGCACACAGGGCCAGCTGATGACGGTGCCACAAGATCCCCATCAATAGACAGCATTCAGAAGGACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026991:ENSMUST00000102754:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.656 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGAGTTCCTATGCCAGTCA
R:
CTGTGTGCTGCAGCCTGTTAT
Band lengths:
344-1747
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