HsaINT0134358 @ 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
chr4:87693931-87695684:+
Coord C1 exon
chr4:87693931-87694111
Coord A exon
chr4:87694112-87695525
Coord C2 exon
chr4:87695526-87695684
Length
1414 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TTACTGCTTTTTTCCCTTAGGAA
3' ss Score
11.65
Exon sequences
Seq C1 exon
TAATCCTTCCCCTCTACCACCGGATATGGCTCCTGGGCAGAGTTATCAACCCCAATCAGAATCTGCTTCCTCTAGTTCGATGGATAAGTATCATATACATCACATTTCTGAACCAACTAGACAAGAAAACTGGACACCTTTGAAAAATGACTTGGAAAATCACCTTGAAGACTTTGAACTG
Seq A exon
GTAAGTTGTTTTCTCTATATTTAAAAAAAAATCCATATTTTTTAAAAGAAGGTGTGTTCATAAAGTTTCCCTTTAGGGAAAAAGCTATCTTTAAAATAGCTTCATATGTGTGTCTAATAAATGGATAACATATCTGGTATGTTTCTGTGCTGAGAAATTAGGAAATAAGGCAAAAAGACCTGAGTATAAATCCTGACTCTACCACTGACTTGCTACAATTTGGCAGACTCCTATGGACCAATCACTTAATTCTTCTGAGTCTTGGTAACTTTGACTATAAAATGGAGCAAGTAACCTCACAGGGTTGTGGTGAAGATTAAATGAAATAACATATGTAAAGCACGTAGTATAGTATCTGCTACAGAGTAGACCCTTAGTAAATATTATTTTTGTCTGCTTCTCAAATTCTGATGAGTTACCTATTTGATTTTTAACCAAGTTTGAATGTAATTTTTTTTTTCTCCTCCACACTTTTTTTGTGTGCTCAGATGGAATCCTTTACATTGTAATAATAGTCCTAGAACTTCTAAACCTACAAATAAGATTTAGAAACAAAATTTCCAAGTATAATATCCTTTACATTGATTGAAAGTTAGCCTTTTTAAATACTGCTTTTATTATCCAAGTAATAAATGTTTATTGTAGAAAAATTATTAAGGAGAGAAGAAGATTAAAGCCACTATAATCTGATTACCCCAAAACTGTTAACATTTTGGAGCTAAATTTCCAGTTACCCTTTTTTTTTTGCCTATAATTGTGCATGTGTGTATTGGAGATGAGGGGTGTGCAGCATCTACATCTTCAGTTTCATTCTTAGCAATAGAGTAAAAATAATCTTTAATTTTTCTTAGAAATCTTTCACCCTTGTAAACAACCTCCGTGTCTCATTTGAAATCTTTTAAAAGTATATTTTATTTATACAACAAAATTAATAAGATTGTGATAATCACCGAAAGACTTCATATTTTTACCAAAAAAAAAGCTTTGTTGTGGCTCTTTGCATCTGTTTAGAAATATATGGCTCTTTGCATTTGTTTAGAAATATATGAATTTTTTTTCTGAACCTTTCCTCCAGAAAGTATTTTTTGATCATCAAAGTATAACCACTATTGTGTCCTTATTTATCCTAAAAATATAAGAAAGAAAGCAGGAGTAAATTCTGTCTCTGCTGTCTCTAGACAAACATAATGTTGTGCTTAAACATAACTTTTACGTGGGATGCAGTGGGGGGACAGTCTGTCTAGAATCAGACAGACTGTCTAGAGTCAGACAGACTTGACTTCTTCACTTGGACAAGTTAAGTAACCTTTTAAGGTTTGACTTTCTCCTCTGTTAAGGGAAATGATAGTCATCTTTCTGTTTGTCTATAGTGCAGAATAGACAACCTAAAAGTATTACTGCTTTTTTCCCTTAG
Seq C2 exon
GAAGTAGAACTCCTCATTACCCTAATTAAATCAGAAAAAGGAAGCCTGGGTTTTACAGTAACCAAAGGCAATCAGAGAATTGGTTGTTATGTTCATGATGTCATACAGGATCCAGCCAAAAGTGATGGAAGGCTAAAACCTGGGGACCGGCTCATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629-PTPN13:NM_080685:32
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.852 A=NA C2=0.113
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(60.8=90.6)
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:
AATCCTTCCCCTCTACCACCG
R:
CTTTATGAGCCGGTCCCCAGG
Band lengths:
339-1753
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)