MmuINT0128824 @ mm9
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103983715-103985238:+
Coord C1 exon
chr5:103983715-103984172
Coord A exon
chr5:103984173-103985106
Coord C2 exon
chr5:103985107-103985238
Length
934 bp
Sequences
Splice sites
5' ss Seq
CAGGCATGG
5' ss Score
2.23
3' ss Seq
CTTTGTTTTTCTTCGTCAAGGAA
3' ss Score
5.91
Exon sequences
Seq C1 exon
TGCCTTCTACTCCTGTTCATTTTGCCAATGGGATGAAAAGCTACACAAAGAAACCGGCATACATGCAGGACAGTGCTATGGACCCATCAGAGGACCAGCCCTGGCCACGGGGTACTCTGAGGCACATCCCAGAGAGTCCCTTCGGGCTGTCTGGGGGCCTGCGGGAGGGAAGCCTCAGTTCCCAAGATTCCAGGACTGAAAGTGCCAGCCTATCCCAGAGCCAAGTCAACGGCTTCTTTGCCAGCCACTTAGGCGACAGAGGCTGGCAGGAACCACAGCATAGCAGCCCATCGCCATCTGTGACAACCAAGGTCAACGAGAAGACCTTCTCCGACAGTAACCGAAGCAAGGCCAAGCGGCGAGGCATCTCCGATTTGATTGAACACCTCGACTGTGCTGATTCCGACAAAGACGATTCCACTTACACCAGCAGTCAAGACCATCAAACGTCAAAACAG
Seq A exon
GCATGGTTTAATTTTAATCCTTTGAGGAGAGACACTGTGTTTTCATTTAACAGAGCAGAGAGATGGTACATCCGTTAGAGAGGGGCATGGCCTGCTAGGATGCTCACGTGGTTCTGGGAAGGAAGAAGCAGCTCGTATCTTCCTCTTCTAACTGCTGCTGCATTTGATGCTGACTGGCAATCCAAGGCTTTGAATGCTAACCCTGAAGTGGCTATGCTCCGATTAAGTTTCATCTCCTACATATTTAAACACATGTCAGTAGAGAACTTTGATATTTGCAGAGCTGCTCGTGGATGGTTCATAGTATGAGCAGTCAGATTTGCCCCAGACCACCTAGGATCTTCTGAACTTTTGTGTGGGAGAAAGCAGCGGCAGGGGGATAGCCTCATTCTCAACATGATGGGAACGTAAGCTCACATTCAGAAGCAGTTTCAGAGGGAAGCTCACAGCTCTGCTTCTGGGGGTGGGGGGGTGGGTGTGGATACAGGGGCATTCCACACGGAAGCCCTCCACCCTCAGGAAGAGAGCGCTGAGCTAACATTTAGACTTTGTTTGCACGCAGGAGCAGAGTAAGCCTGAGGCTGGCTAGCTTAGACACCAATTAGTCTGCTTCCTTGGTACATACAGACTCCTAAAGAAAGTGGGCATACATCAAGCCCAGGACCCGGAGGCATGGGCAGAGGCTCTTCCGAAGCTTAAGTTCTGTTTCCTTCCCCCTGGTCCAGCTTCACTTTCTGAGTGTCAGGTGTCTAAACAAAATGAGTGATTCCTGACCTGACAGTGTCTGGAAAGCCCCCAGCCTTCATGGTCTTGATATACTCTATTCCTTCACGCCTTGATTTAGAAAAAAAAATTTTTTTTCAAAAGTGTTTGTTTGCAGTAAGAGTTCGTTTGGGCTCTAATGAGAGATCCTCCTTTGTTTTTCTTCGTCAAG
Seq C2 exon
GAACCTTCCTCCTCACTGAGTACATCGAACAAAACGAGCTTTCCAACCTCGTCTGCGTCACCTCCTAAGCCCGGAGACACGTTTGAGGTTGAGCTGGCTAAAACTGATGGCAGCCTGGGGATAAGTGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573-Ptpn13:NM_011204:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.980 A=NA C2=0.955
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(18.1=34.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCAAGTCAACGGCTTCTT
R:
AGGCTGCCATCAGTTTTAGCC
Band lengths:
357-1291
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: