HsaINT0134350 @ hg38
Intron Retention
Gene
ENSG00000163629 | PTPN13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:HGNC Symbol;Acc:HGNC:9646]
Coordinates
chr4:86764593-86765488:+
Coord C1 exon
chr4:86764593-86764724
Coord A exon
chr4:86764725-86765394
Coord C2 exon
chr4:86765395-86765488
Length
670 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTG
5' ss Score
5.88
3' ss Seq
TTTTGTCTTTTTCTCTTTAGGGA
3' ss Score
12.52
Exon sequences
Seq C1 exon
GAATCTTCCTCTTCAGTGAATACATCCAACAAGATGAATTTTAAAACTTTTTCTTCATCACCTCCTAAGCCTGGAGATATCTTTGAGGTTGAACTGGCTAAAAATGATAACAGCTTGGGGATAAGTGTCACG
Seq A exon
GTACTGTTTGACAAGGTTTTCAAATGTTTTCTCTTCTTTAATTTCCAGCAGCCTATTGTATGTCAACTTTTTAATTGAATTATTTTGCATCAAAAGGGACACATCAAATACCTCCAAAATTCTAAAACTGAATCATATCTAAAAACTATTTTAAAAATTGTGTTAGTCACTTTTTCCTGTGATTTTAAAAAAATTAGACAAACACTACCTTTTTCTCCATAGATTTAATACTTGCTTTATCTGAATATAAAACTTGCAAATTGTAAAATTAATGTAATGCTTTGTAGATATTTGACAGTTTCTACGTGAGCATAGATTATATATCTCTAACCTACATTATTAGTAATTAAAGACTGTATATTTCTGTATACTCTCCATAATATGTAATACCTTGTAAACATGTTAGTATCTTAAAATTAGAAGTTCCCAAGGAATATATGTATCTTTAAGGTAGTCAGAATGTGAGCATAGGCTATTTGATAAAATTATTTTTGAATTATACTGATGAATATAATATCCCTCATTAGTATACTAATGAATATACTGTACATCAGCACATGCTGATGGGATGTCACTGCTTTGGCTAATGAATCCTTTCTAGGCCTGAGATTTGAAAGAGAGTGCAAAATTTTTCATGTTATAAAATATTATTTTGTCTTTTTCTCTTTAG
Seq C2 exon
GGAGGTGTGAATACGAGTGTCAGACATGGTGGCATTTATGTGAAAGCTGTTATTCCCCAGGGAGCAGCAGAGTCTGATGGTAGAATTCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629:ENST00000427191:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.843 A=NA C2=0.510
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:
ATCTTCCTCTTCAGTGAATACATCCA
R:
TTGTGAATTCTACCATCAGACTCTGC
Band lengths:
222-892
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