MmuINT0128810 @ mm10
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103525754-103526114:+
Coord C1 exon
chr5:103525754-103525828
Coord A exon
chr5:103525829-103525933
Coord C2 exon
chr5:103525934-103526114
Length
105 bp
Sequences
Splice sites
5' ss Seq
CTCGTAAGT
5' ss Score
9.63
3' ss Seq
TAATAAAGACTTCTTTTCAGTCG
3' ss Score
0.65
Exon sequences
Seq C1 exon
AATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTC
Seq A exon
GTAAGTAGTAACTCCAGCTTCTGTCCCTCTGAGGGCATGTGTCCCGTGATCCTCTAAAGCAAGTCTAAGTGGTCGAGGGCTGCTTTAATAAAGACTTCTTTTCAG
Seq C2 exon
TCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573:ENSMUST00000048957:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.082
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF093795=FERM_N=PU(49.4=72.1)
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:
TTTCTTTGGACCTGAGTTTGTGA
R:
CGAGAGCAAACAAATGGTGCT
Band lengths:
242-347
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