HsaINT0134353 @ 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
chr4:87688970-87691136:+
Coord C1 exon
chr4:87688970-87689129
Coord A exon
chr4:87689130-87690921
Coord C2 exon
chr4:87690922-87691136
Length
1792 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
TTTTATATCTTTTTCTCCAGAAA
3' ss Score
10.14
Exon sequences
Seq C1 exon
GTGGTTCATCTGTTATTAGAAAAGGGACAATCTCCAACATCTAAAGAACATGTCCCGGTAACCCCACAGTGTACCCTTTCAGATCAGAATGCCCAAGGTCAAGGCCCAGAAAAAGTGAAGAAAACAACTCAGGTCAAAGACTACAGCTTTGTCACTGAAG
Seq A exon
GTCAGGCCTTGGGAGACTACAATCTCACCTTTAAATTATTCCTCGCCTATTCAAAATTTGATTTTTACATGTTGGATTACAGTTAATGCCCTAGTTTTGTTCATTATTCTTGTCAAGTACAAATAATAATCTGACATCACACCATACTGAATAAAGACAGAAACATATTTGCAGCTCATAGGGTCTGAAAGACTTTGGATAATAAAGTCATGCATGATTATGGTCTTTTAAAAATGCTTTAAATTGTTGTAAAATTCAAAATAGAATTTGGTAAGTGAAAAAATAAAGAAAAACAAATGCTGAGATGCCTTCAAACCCATGGGAAACCTTGACCCTTAGATTTTTGTATTTCTATTTAATTTAATTTTAAGAACTGTGAATCAAACTCTGGGCAGATATTCACATAGTAGTGCCCAGAAAGTGGTCTTTGTTACAAACTATGCTAGCCTTTGGACAGATCACTAATTGGTAGTAAGAAAATTAAGAATGACAGTGGCTTTCCAGTACCCTTTAAGATTCTGTCTTCTTAAGAGGTTTATATTTCCTTTACTTTATAAATGATGGTGATGGTGTACAGTCATTGTTTTATTTTACACAAACGTTAGCAACTCTGAATCAGTCCCCAAAATAATGAGAAAAAATAACACAGACTATATTATTTTTTCCTGAATATGAAAATAAAATTAATGTACTCATTTTATCATACTGCTCTTTATTCTTTATTTCTTCCATCTTTTTTTTTTTTTTTTTTTGAAACAGAGTCTCGTTCTGTTGCCCAGGCTGGAGTACAGTGGCGCAATCTTGGCTCACTGCAACCTCCGCCCCTGGGTTCAAGCTATTCTCCTGCCTCAGCTTCCTGAGTAGCTGAGATTATAGGCACACACTGCCACATGCGGCTAATTTTTGTATTTTTAGTACAGACGGGGTTTCACCATGTTGGCCAAACTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCCTCCTCAGCCTCCCAAAATGCTGGGATTACAGGTGTGAGCCACCACACCCAGCCCCATCATTCTTTCTTTAAATAGATTTTTTTTTTAAACACCCAAGCCAACCATGAGCAAAGACTTTAAATGTATTTTTTAATTATTTTCTGGTTATTGTTCTTTTAATTTATTTAGCTGATAAGAAATTTATTGAAATATTGCAATTTATCTGAGTTAAATTACACCTCCCCAGAACATTACAATTTCAATTTATTTCCACATAACCTCCTCTAACATTTATTTTGTTCTTCTTTTCATCTTTCTCACGCTGTATACCTGAGTTTCTCCCATACCTGTCCTTCTGTGGAGTTTCCCCTTTTTTTGTCTGTTATCGTACTCTGTTTTGTTTTGTTTTTGTAGAGATTGGATCTCACTGTATTGCCCAGGCTGGTCTCAAACTCCTGGGTTCAAGCAACCCTCCTACTTCGGCCTCCCAAAGTACTGGGGTTTATAGGCATGAGCCACTGTGCCTGACCATAGTGTCTTTTAAAACACACAAGTTTGATGCATAATTCCATTTTCAGAATCCTACTTTCAGAACTCTCCTTCCTAATCAAACAGCTTAGTTCATGCAGTTAGTTGATAAGATTTCTTAATGATGGAAATAGACTGTAAGATACAGCTTCAGTATACCATTGGAGTGCAGTAAGTACATACAGAGCTATAAATACGGGAAAATGGGCTTTTAAAATGTGTCTAGAAGTATATATGTTTGTATGTTCCTATGTAAACACAGCATGTTAATAATATCTAAATTTTTTTTATATCTTTTTCTCCAG
Seq C2 exon
AAAATACATTTGAGGTAAAATTATTTAAAAATAGCTCAGGTCTAGGATTCAGTTTTTCTCGAGAAGATAATCTTATACCGGAGCAAATTAATGCCAGCATAGTAAGGGTTAAAAAGCTCTTTCCTGGACAGCCAGCAGCAGAAAGTGGAAAAATTGATGTAGGAGATGTTATCTTGAAAGTGAATGGAGCCTCTTTGAAAGGACTATCTCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629-PTPN13:NM_080685:28
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.694 A=NA C2=0.028
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PD(7.2=11.1)
A:
NA
C2:
PF0059519=PDZ=PU(78.8=93.1)
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:
AGAAAAGGGACAATCTCCAACA
R:
AGTCCTTTCAAAGAGGCTCCA
Band lengths:
348-2140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)