HsaINT0134350 @ 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
chr4:87685746-87686641:+
Coord C1 exon
chr4:87685746-87685892
Coord A exon
chr4:87685893-87686547
Coord C2 exon
chr4:87686548-87686641
Length
655 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTTC
5' ss Score
0.45
3' ss Seq
TTTTGTCTTTTTCTCTTTAGGGA
3' ss Score
12.52
Exon sequences
Seq C1 exon
GAATCTTCCTCTTCAGTGAATACATCCAACAAGATGAATTTTAAAACTTTTTCTTCATCACCTCCTAAGCCTGGAGATATCTTTGAGGTTGAACTGGCTAAAAATGATAACAGCTTGGGGATAAGTGTCACGGTACTGTTTGACAAG
Seq A exon
GTTTTCAAATGTTTTCTCTTCTTTAATTTCCAGCAGCCTATTGTATGTCAACTTTTTAATTGAATTATTTTGCATCAAAAGGGACACATCAAATACCTCCAAAATTCTAAAACTGAATCATATCTAAAAACTATTTTAAAAATTGTGTTAGTCACTTTTTCCTGTGATTTTAAAAAAATTAGACAAACACTACCTTTTTCTCCATAGATTTAATACTTGCTTTATCTGAATATAAAACTTGCAAATTGTAAAATTAATGTAATGCTTTGTAGATATTTGACAGTTTCTACGTGAGCATAGATTATATATCTCTAACCTACATTATTAGTAATTAAAGACTGTATATTTCTGTATACTCTCCATAATATGTAATACCTTGTAAACATGTTAGTATCTTAAAATTAGAAGTTCCCAAGGAATATATGTATCTTTAAGGTAGTCAGAATGTGAGCATAGGCTATTTGATAAAATTATTTTTGAATTATACTGATGAATATAATATCCCTCATTAGTATACTAATGAATATACTGTACATCAGCACATGCTGATGGGATGTCACTGCTTTGGCTAATGAATCCTTTCTAGGCCTGAGATTTGAAAGAGAGTGCAAAATTTTTCATGTTATAAAATATTATTTTGTCTTTTTCTCTTTAG
Seq C2 exon
GGAGGTGTGAATACGAGTGTCAGACATGGTGGCATTTATGTGAAAGCTGTTATTCCCCAGGGAGCAGCAGAGTCTGATGGTAGAATTCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629-PTPN13:NM_080685:25
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.675 A=NA C2=0.469
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:
AATCTTCCTCTTCAGTGAATACATCC
R:
TTGTGAATTCTACCATCAGACTCTGC
Band lengths:
238-893
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)