MmuINT0128825 @ mm10
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103556088-103557972:+
Coord C1 exon
chr5:103556088-103556219
Coord A exon
chr5:103556220-103557878
Coord C2 exon
chr5:103557879-103557972
Length
1659 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTG
5' ss Score
5.88
3' ss Seq
ACTTTGTTTTGTCTATTTAGGGA
3' ss Score
10.65
Exon sequences
Seq C1 exon
GAACCTTCCTCCTCACTGAGTACATCGAACAAAACGAGCTTTCCAACCTCGTCTGCGTCACCTCCTAAGCCCGGAGACACGTTTGAGGTTGAGCTGGCTAAAACTGATGGCAGCCTGGGGATAAGTGTCACG
Seq A exon
GTACTGTTTGACAAGGTTCACGCCTTCTCTTCTTCACCCCCAGCAGACCGTTGTAGCCCAACCTGTTAGCTGAGTTACAGTGGCTCAGATGGGACACTTATCAAATGCTTCCAAAAGCTAAAAATTGACTATCCGAAAACTCCTTTAAAATGTGTACGCTACTCTTCCCCTCCACCCACTGTGGTTTAAAAAAATTGGGAATTGCTTGTTCTCCATACATTTTTTTACTTGCTTAATTTAAGCATATCATGTGCAGAATATGAAATGTATGGTTATTTTTCGTATATTTCTAACAGTGAAATCATGAGATGACATCTCTTTAATCTATCCCGTGAATAACTAAAGAATGTGGATATTTATCTGCTAACTCTCTCCAAAATACATATTACCTTGTAACACATTTAAAACCTTAAAAGTAGAGGTTCCAAACTGTCCATATATCTTTAAGACCACAGAGATATCTACAAAGACTATTTGATAACATTATATTACAGTTCTATAATATGTTATCCAGGAACTGCAGCTTTATATTTGTCACAGTCTAAGATCACTGGTCATTACATAAAGCCATTAAAGATGTGGTTGAGCCAGCATGGGAGGTGACTCAGGGGGATCAGTTACCAACACCCACATTAAAAACAACCAAAACAGGATACACAGTGCACAGTGCAACCCTGCACTGGGGAGACAGAAGGGTTCCAGGGCTTGCTGATCATCCAGTCCAGCCCAGACAGCAGGCTTAGTGTTCAGAGAGAGACCCTAACTCACAAATCAGAGAAGCGATTCAAGAAGACTCCCCGCATCAACCTCTAGACTAGCATGCACGCTCATGAATGTACACATGCACACATGCATGCACATGCATTAATGTCACCTGCACGGATTTGTACATGCACACCCGTGAATGTGCACCTCCATGCATGCATGCACGCACAGGCATACACATGAATGTACACCTGCATGGATGTGTGCATGCATACAAATGAGTGCACACCTTCACAAATGCGTGAATTCATGTACACACACACCTTTTCTGCATACACATGAATGTACAGCTGCATGGATGTGTGCATGCATACAAATGATTGCACACCTTCACAAATGCGTGAATTCATGTACACACACACCTTTTCTGCCAAAGACTTCATTTTTTAGTTTAGTTCAGGTTTTTGGGTTTTTTGTTTTTAGTTTGTTTTGTTTTCTTCTGTTGTGTTTGTTTTGAGACTGAATCTATCCATGTAGCCCTGCCTGGCCTGAGATCACTTGCCTCTGTCTCCCAAGTGCTTGGATTAAAGGTGTATCCCACCATCCTCAGGCTTTTTTACATCGCTTTCTGCTTGCTCATGATGCGGGACCCAGAAAGGGGCACCAGTTCCTTACGAGTCAAGACGCAGCATAGTGACACTTTCTGGACTCAGTAAAGAGGAGAGACAGACAGACCGACTCGGAGAGTCAGACTGAAAGAGAGAACAACAAAAGAGCAGGCTGCCTTCAACATTTGGGCTGTAGCTAGCAGTGCTACTGGGCATTCAGATACTTTGAACGTGCTGATGTCGAGTTAGCTTTGTCTGGTGATTTGAACCCTTTTTAGCACTTAACCTTTGAAAGCATGCAAATTATTTTCATGTCAATACGTGCCACTTTGTTTTGTCTATTTAG
Seq C2 exon
GGAGGTGTGAATACCAGCGTCCGACATGGTGGTATTTATGTGAAAGCCATTATTCCCAAAGGAGCGGCAGAGTCAGATGGCAGAATTCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573:ENSMUST00000048957:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.955 A=NA C2=0.594
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PU(18.1=34.1)
A:
NA
C2:
PF0059519=PDZ=FE(37.3=100)
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:
GAACCTTCCTCCTCACTGAGT
R:
TGTGAATTCTGCCATCTGACTCTG
Band lengths:
223-1882
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