MmuINT0128825 @ mm9
Intron Retention
Gene
ENSMUSG00000034573 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:MGI Symbol;Acc:MGI:103293]
Coordinates
chr5:103985107-103986991:+
Coord C1 exon
chr5:103985107-103985238
Coord A exon
chr5:103985239-103986897
Coord C2 exon
chr5:103986898-103986991
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-Ptpn13:NM_011204:25
Average complexity
IR-S
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
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: