HsaINT0134348 @ hg19
Intron Retention
Gene
ENSG00000163629 | PTPN13
Description
protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) [Source:HGNC Symbol;Acc:9646]
Coordinates
chr4:87679831-87680226:+
Coord C1 exon
chr4:87679831-87679938
Coord A exon
chr4:87679939-87680094
Coord C2 exon
chr4:87680095-87680226
Length
156 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTT
5' ss Score
8.17
3' ss Seq
TGGATTGTCTATTTGTACAGGAG
3' ss Score
5.27
Exon sequences
Seq C1 exon
GATTTCAAATTATTGGTGGGGAGAAGATGGGAAGACTGGACCTAGGCATATTTATCAGTTCAGTTGCCCCTGGAGGACCAGCTGACTTGGATGGATGCTTGAAGCCAG
Seq A exon
GTACTTTACATTTTGGTAGTTTTCTAAGTATTTTCTGACAGGCATGAATTTAGGAACTTAGGCCAAACTAAAATAATTGAGAAAGAGATGATATTTCTAAGATTCAGAATAAATGTATCTTTGTTGTTGAAAATACTGGATTGTCTATTTGTACAG
Seq C2 exon
GAGACCGTTTGATATCTGTGAATAGTGTGAGTCTGGAGGGAGTCAGCCACCATGCTGCAATTGAAATTTTGCAAAATGCACCTGAAGATGTGACACTTGTTATCTCTCAGCCAAAAGAAAAGATATCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629-PTPN13:NM_080685:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0059519=PDZ=FE(42.9=100)
A:
NA
C2:
PF0059519=PDZ=PD(41.7=77.8)
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:
AAATTATTGGTGGGGAGAAGATGGG
R:
CTTTGGATATCTTTTCTTTTGGCTGA
Band lengths:
234-390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)