MmuINT0128844 @ mm9
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:104015725-104017210:+
Coord C1 exon
chr5:104015725-104015828
Coord A exon
chr5:104015829-104017061
Coord C2 exon
chr5:104017062-104017210
Length
1233 bp
Sequences
Splice sites
5' ss Seq
AAGGCAAGG
5' ss Score
2.76
3' ss Seq
CTTCTGGTCCTTCCTGATAGATC
3' ss Score
9.51
Exon sequences
Seq C1 exon
CTTAACTGCAGCATCACAAGAAGAGAAGCCCATCGAAGAGGACGCCACGCAGGAAAGCAGAAACTCGACAACGGAGACAACAGACGGTGAAGATTCCAGCAAAG
Seq A exon
GCAAGGATTTTAGGACCAGCTTCTTGCATTTAAAACAGCAAGCAGGGAGGTGAAAGCTCTAAGTGATGATTTCACAATTCATGGATGGTATTGCCGAATGTATATGCTCTTTGGTGTTACACATACACGGCATATACACATATACGATGTCTAAGTCACGTAGACATCGGCTTTGGTGGCCATAACTAAATTATTTGCATAGCTAGAGCCTAAAGCTCTCGGTGGCTTAGGGGAAAGCACAAAGTATCGTGACTTAAAAATGGAAACTGCAAGTCTTGGTTCTGCTGTGGACTAGTGAGAGATAAGGAGCTCAGCTCGCCGGGGACAGAGCTGCTGCGACATCTGAAATGCGAGAGAGAAGTTGCCCTTGACTGCTGGCCTGGCTTTTTCCGGCCCGCTCTGTCCTTCTGCAGGCTCCTGTGGACACCTGCGGCATACTCTTCCAATTAGCTTTCCTGCTCCAATTGCAGTCCTGTTCTTCAGAAAGAGTTAACATATTTCAGATGAGCAGAATGGATCCCCACTGACCATGCCCCACCAGGCGCTGAGCTCCTTGGGGCATCTTGTCCAGCCCTGGATCCCTCATGGCGCTCAGCCTTACTGCCCCCTGCAGGAAGTTAGCTGCAGCACCACCATGCCCTAACTGCTTGAGGATTCTCCCGCCTTGTCTGGGAAAGCAATTGCCTTGTGTTGTAAATAATCCGTATAGCGGGTACTCACTCAGACCCCAGGCTCTTCTAGGGTACCTGTGTAATACAGCTCCTAAATAGTCCACGAAAAGTGCTCTGTGCAGGAAGAACACTGCCCAATCCAGGAGTCGGCAGTGAGGGGGAAGAGGAGGCACGGAAAAGGGAAGGCTGTAGTCTAATGACAATCTCCTCACGTGTGGGATTTCTGACCTCTTGTCTCTGTCTTCCCCAGTGCTGAGAATCCAAGTAACAGGGGAAACTGGGTAGGTTTTCCTCACATAAACAGTGTCAGTAAAGTCAAACAAAAATGAGCATATGTTCCTTTCAAGAGCTAAACAACTGGGAGTCGCCCGCCTTCCAGACCTGTGAGCAGTGATGAGGTAGCTGCTTCAAGGCTGGGTGAGGTAGCGGTGTAGTAGCAAAACCTGTGTGGCCTGCAGTCATCAGCCAGGCTGCTGCCCCCTTTCCTAGGACAGTGGGAAGTGAGAAGAGGCTCAAGTGAGCTCGGGTGAGAACTGAAGAACCTTCTGGTCCTTCCTGATAG
Seq C2 exon
ATCCCCCCTTTCTGACGAATGAGGAGCTGGCAGCCCTGCCGGTGGTCAGAGTCCCTCCCTCTGGCAAGTACACGGGCACACAGCTGCAGGCCACCATCCGCACGCTGCAGGGCTTGCTCGACCAAGGGATCCCTTCTAAGGAGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573-Ptpn13:NM_011204:42
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.640
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACTGCAGCATCACAAGAAGAGA
R:
TCCAGCTCCTTAGAAGGGATCC
Band lengths:
248-1481
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: