HsaINT0134337 @ 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
chr4:87653745-87655609:+
Coord C1 exon
chr4:87653745-87653919
Coord A exon
chr4:87653920-87655455
Coord C2 exon
chr4:87655456-87655609
Length
1536 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCA
5' ss Score
7.87
3' ss Seq
ATTTTTCTCATTCTGTTTAGATA
3' ss Score
8.49
Exon sequences
Seq C1 exon
ACTAAGAAAGGGAAGAATGAGGATAACCGAAGGAAAGTAAACATAATGCTTCTGAACGGGCAAAGACTGGAACTGACCTGTGATACCAAAACTATATGTAAAGATGTGTTTGATATGGTTGTGGCACATATTGGCTTAGTAGAGCATCATTTGTTTGCTTTAGCTACCCTCAAAG
Seq A exon
GTACCAAGACATTTTATATTCAGAGTACAGTATAGAAATTTAGCAACAAGCAGACTTCCTATGTTTGTTACCATGCCTGACCTCATTTTGACAATTAGTAACTAAATGAACTAGTCAGTAGAAGTGAGTTAGGAACTCCCTTTCTTCTCCCAGCTACTTTCATTGTTTTAATAGTTATGTTTGTTAGGCACCTTCTGTATCTGACTGGGAAGATTTTTTTATTTTTTGCTATGGTTATATAAAAATATATTTTAATTATATTTTAGGGACCGTTTTATATGTTAATGGTCTACATGTGTACTCTAGAAATTAGTATCCTAATATGAGCCTGAATGTATAGCAAGACCTTATTTCTGAATTTCCACATCAGTTTATTTAGTCTACTATCCTAAAATCACAGTGACTTTTTAAAATGTCAATTGAAGGCTAAAAATTAGTTATTTCACATTATCTTTTAAATATTGTATCCACTTAAACCCATGATGTTCACAACCACAGTGGTCTAAGACACAGCTTCAGTAGAAACTTCTCCTATTTATCAATTAGAGTTGCCATAGCAGTAAGAAACTTTTTGGAATTCATCTCCTTTTTAAATAAATCATTATATTTATAAATTACTCTTTAATATTTCAGATTCCTGTTTACCTCAAAATTTAACTTGGAAAGTTTAGGCAACAAAGTACTATAAATGACAATTGACAGGTTAAAGGATCCTAAAACTCTATAAGCTCTTAATATCTTCTGTATCCTAAAAGAAATATTTCCCTCAATATAGCTTATTGAATTATTGTGCCTTAAAAATGAATAATTTATGCTGTAGACTCATACAATAAATAGTCAATTAGTACCTACTGATGTTCTATCACTTTACTAGTTTCACTTTTAGACTAATCAGTCAATATTGTCTACATGAAGCTGATTCAGTTCATCCAAATATCTATTTATACTATACCTAATTTCTTACAGATTCTGGTAAAATCAAATTGTATTGAATAATTCTTTTATTTGTAGAGAGTAAATAATAGTTAACTAATGACATTAAAAAATAAAATGATAAATGTCATTCCTTCTAGGTTTCAGCTGGTAGCTCAATAATAATAAGTATACTAGCTAATATTTATTAAATGTTTACCGTGTACTGTGTGCTTTAACAAGTGTTTTTATTCATTATGTCATTTGATCCTTATAACAATGCTGTAAAGCAAGAATTCCCACTAGCCTGATCTTAAAGCCAAGAAAACTGATGTCTAGAGAGGTAAAATAATATATTCAGTGTCATACGGATAGTAAATGTTGTGACCAGGTGTTGAATCTAGGACTGTATGTCTTTAGAGCCGCCATTCTTAAAAGAGTGGGCCATATTGCCTCCCATCTAAATGGAGTGTCTCAGAGCTCCCTGCCACATTTTTAACAGTCTTGTATTTATATTCTCATATGATACTCTTTTATGCAAGTCTGACCAAAAAGTGAAGAAATCGGAAGAAAACACTAAAGTATTTTTTTATTTTATCTGAATATTTTTCTCATTCTGTTTAG
Seq C2 exon
ATAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCAGAGGGATGGAAAGAAGAACCAAAGAAAAAGACCAAAGCCACTGTTAATTTTACTTTGTTTTTCAGAATTAAATTTTTTATGGATGATGTTAGTCTAATACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629-PTPN13:NM_080685:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF093795=FERM_N=PU(49.4=74.6)
A:
NA
C2:
PF093795=FERM_N=PD(49.4=84.6),PF0037313=FERM_M=PU(5.1=11.5)
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:
ACTAAGAAAGGGAAGAATGAGGAT
R:
ACAAAGTAAAATTAACAGTGGCTTTG
Band lengths:
286-1822
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)