MmuINT0128811 @ mm9
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103954953-103956168:+
Coord C1 exon
chr5:103954953-103955133
Coord A exon
chr5:103955134-103956014
Coord C2 exon
chr5:103956015-103956168
Length
881 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCT
5' ss Score
7.56
3' ss Seq
CCTTTCTCATTCTGTTTCAGAGA
3' ss Score
11.56
Exon sequences
Seq C1 exon
TCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAG
Seq A exon
GTATCTCCATGTTTTGATTCAGAGTTCGCAGTGGAAAACCTGGCATCAAGATGGCACCCTGGACCTCTTATTGAGCCAGGCTTCATTCGGGGGCGGGGGAAAGAGTAATTAAATAGGCAGGACGGTGGACGCTGAGAAGGAACAGAAGGCACTTAGAGACTTTTTCCCAGTTTCATTTATTGTGTTTGTGAGGCTCTTTCCATATCTATGTAGATTTTTTTAAATGCTTGTGCCTTAAAAATGAATAATTCATCCTGTAGAGTCACCCATTAAGTGTGCAATCAGTACTTTTTTTTTTTAAATCTCGATTTAAAATAAAGAAATGTAGCCCCAGAGGGGTGGAAAGAGCTAGGACCTACCTCTAGGACTTACTCACCCCACCCCCATCCTGGACTGACCAGATAGTGTTGTCTACCCGCAGATACCTTTGAGACAGATCTCTTAATTTCTTAAACATTCTGTGCACGTCAGGCTTTATAGACCAGCTGTTTAATTAGTGACTACTAGCTAATACTCACTGCAGACCTGTGCTCTAAGGGTTGGCTTCCAGCGCACTTTATTTTGTCATTGGATTATTATAATATCCTACAGTGCAGAATCTAGCATCATCCTGGTCTTACCGACAGGGAGATCGATGCCCGGGGTGGAAGAGGAATTTATCTCACGGGCAGTAAGACATGGCTGGGATCTCAGTCCAGGTCTGCCTGTCTCTGTCTGCTTTTGAAGACTGATCCACACTGAAGCCAGCCTTATGCAGTGCTCAGCCCCTGCTGTACTTCTGAAGGGCCTTGTTCTTTTTTTTTTTAATACATTCAACAGAGATGAAGACATCAAAGGAAAACTCTCCATGCTTGCTGAATGCCTTTCTCATTCTGTTTCAG
Seq C2 exon
AGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034573-Ptpn13:NM_011204:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF093795=FERM_N=PU(49.4=72.1)
A:
NA
C2:
PF093795=FERM_N=PD(49.4=84.6),PF0037313=FERM_M=PU(4.3=9.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAGACCAAGAAGGGGAAGA
R:
TGTATCAGACTAACATCATCCATGA
Band lengths:
334-1215
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: