MmuINT0128822 @ mm10
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103550749-103551178:+
Coord C1 exon
chr5:103550749-103550856
Coord A exon
chr5:103550857-103551046
Coord C2 exon
chr5:103551047-103551178
Length
190 bp
Sequences
Splice sites
5' ss Seq
CTGGTACTT
5' ss Score
4.74
3' ss Seq
TTGGATGGTGTATTTTCCAGGAG
3' ss Score
7.08
Exon sequences
Seq C1 exon
GATTTCAAATTATCGGTGGGGAAAAAATGGGAAGACTGGATCTAGGAGTGTTTATCAGTGCAGTTACCCCTGGAGGACCTGCTGACCTGGATGGATGCTTAAAGCCTG
Seq A exon
GTACTTGACATTTTGATAATTTCCCATGTGCTTTCTAATGAATAAATTTGCACAGAGGACAAAATGTAGACAAAACAACAACAACAATAATAATAATAATAATAAATGATAGTGAGAAAGGGTTAAATTTCTAAGGCTTGATATGAGCATTGCTTTGTTGCTGATGGACATTGGATGGTGTATTTTCCAG
Seq C2 exon
GAGACCGTTTGATATCTGTGAACAGTGTGAGTCTGGAAGGGGTCAGTCACCACGCTGCAGTGGACATTCTGCAGAATGCACCTGAAGATGTGACACTTGTCATCTCCCAGCCAAAAGAAAAACCGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573:ENSMUST00000048957:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.205 A=NA C2=0.307
Domain overlap (PFAM):
C1:
PF0059519=PDZ=FE(42.9=100)
A:
NA
C2:
PF0059519=PDZ=PD(41.7=77.8)
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:
GATTTCAAATTATCGGTGGGGAA
R:
ACGGTTTTTCTTTTGGCTGGG
Band lengths:
234-424
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