MmuINT0120935 @ mm9
Intron Retention
Gene
ENSMUSG00000026991 | Pkp4
Description
plakophilin 4 [Source:MGI Symbol;Acc:MGI:109281]
Coordinates
chr2:59146065-59148347:+
Coord C1 exon
chr2:59146065-59146614
Coord A exon
chr2:59146615-59148158
Coord C2 exon
chr2:59148159-59148347
Length
1544 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGCCACGTTCCTATTTCTAGGCT
3' ss Score
8.85
Exon sequences
Seq C1 exon
CCATCAGTAGCCAATCGGGCCATGCGGAGAGTTAGTTCAGTTCCATCTAGAGCACAGTCTCCTTCTTATGTTACCAGCACAGGCGTGTCTCCTTCAAGGGGGTCACTGAGAACTTCTCTGGGTAGTGGATTTGGCTCTCCATCAGTGACGGACTCCCGACCTCTGAACCCCAGTGCTTACTCCTCCAGCACGCTCCCTGCACAGCGGGCCGCCTCTCCATACTCACAGAGACCCGCCTCCCCAACAGCCGTGCGCCGGGTCGGGTCTGTCACCTCCCGGCAGACCTCCAATCCCAACGGACCAGTCCCTCAGTACCAGACCACCACCAGGGTGGGGTCCCCACTGACCCTGACTGATGCCCAGACTCGAGTAGCTTCCCCATCCCAAGGCCAGGTGGGGTCATCGTCCCCGAAACGCTCTGGGATGACCGCCGTACCACAGCACCTGGGACCTTCACTGCAAAGGACTGTTCATGACATGGACCAATTTGGACAGCAGCAGTATGACATTTATGAAAGGATGGTTCCACCTCGGCCAGACAGCCTGACAG
Seq A exon
GTGAGGACAGGTGACGGCACTATACAAACCCCAGGGCGTGAGTCCTCCCTGTGCCTGTGTGGAAATGGTGATCACTGGAGAAAGGCCTAGTGGTCTCCTCTGAAAAGTTACACTGTAAACTTGGGGTACATATTTTTCAAGCATTGGTTCTTTTATGCTTGACACTATGTAACCCATACACAGAACTCTTGTACGGCATCTAAATTTCCCTCAAAATATGGTGCATAAAGTGTGACTCTGTGTATGTGTACACACGCACACTATATTTTAAAAGAATTGATTATAACCCTAAGCTCTTGTTAGTACTATTTTCTAAAGCAGGGTTTTGAACATCTAGGCTTATACCTCCATACACCCTCATGATATGTTAAAATGTGTTATTAGAATGTCTGTTTGAAGCCAGGCATGGTGACGCACGCCTTTAATCACAGCACTCGGAAGGCAGAGGCAGGCGTATTTCTGAGTTCGTGGCTAGCCTGATCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCAGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAATATCTGTTTGAATTTATCTTGAGGAATGCTGTAGTTGTGTGTGCTAAAATATGAATCTCGTACCCTACTGTTTTGATGGGCTCCCTGATGGGAAATGTACAAAGCCCTTATGAATTTTTCTTAAATGCCATTTGGATTAAATTAAAAAGACCCCAGGTTCCTGACATCCTATCTGTCCCCTTTGGGGGATTTTCATAAGAGTTTTTCTACTTTCTGTAATGACATTATTCTTTTTAGTAAGAGTAATTTTTCTTCCAAAAAACTTAGGCATGGGACCTGGGATGTAGGGAGCTGGCAGAGTGCGAGCCTAGCCCTGTGCAAGGCCCTGAGTTTGACCCTATACATTGCCAGAAAAGTTTTTATAAAACACGGTGTGTATAGAATGGAGATATTTGAAACCATAAGGAGAAGGTAAAATGAAAAACACGAGTCTCCAGCTCCGCCCCTCCCCACACCAGTCTCGCTTTCCCGTGTAGTCTACATGTGTGTGACACATGAATGTGCACGTGTGTCAGCCTGTTTTGTTTGTGTGCAAACATAGGATATACTTACACACTAAGCTGAGGATGATGTCACCATGCACCACAGTCTCATGGGAACACTTGGTCCATCCCTGGCCAAGATGTCATTTATGCTGTGCCTGATGCATTGATCTTTAAATGGCAATCGCAGAGAAGCAGGCCCTGCTCTGTTTGGTCACCATGGTAAAGTAACCCATAGTTGAAGAATGAATTTTAGCAAATTAAGCTTAATAAATTTTTATTAGGAAGTCTACTTCTCTCTTGCTAGCAAGAAAGTTTCTTTTGAAAAACACATAGCATACAGAGTCCTTTTCATACCAGGCCTTCCTTCTGTAAAACTTGAGCAGTTTTTATCTTCAGACTCACACTTGTCCTGTTGATTAGGACTTGAATGGGGTATGAGTTTTAAGCTTACCATGATTTTCTCCGTTGTTGATGGTGCCACGTTCCTATTTCTAG
Seq C2 exon
GCTTACGGAGTTCCTATGCCAGTCAGCATAGTCAGCTTGGGCAAGAGCTCCGTTCAGCTGTGTCTCCTGACTTGCACATCACTCCTATCTATGAAGGGAGGACCTACTACAGTCCAGTGTACCGCAGCCCAAACCACGGGACCGTGGAGCTCCAGGGGTCACAGACAGCATTGTATCGCACAGGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026991-Pkp4:NM_175464:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.999 A=NA C2=0.661
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:
ATACTCACAGAGACCCGCCTC
R:
TGACTGGCATAGGAACTCCGT
Band lengths:
357-1901
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: