HsaINT1028470 @ hg38
Intron Retention
Gene
ENSG00000163629 | PTPN13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:HGNC Symbol;Acc:HGNC:9646]
Coordinates
chr4:86762727-86764724:+
Coord C1 exon
chr4:86762727-86763190
Coord A exon
chr4:86763191-86764592
Coord C2 exon
chr4:86764593-86764724
Length
1402 bp
Sequences
Splice sites
5' ss Seq
CAGGCATAG
5' ss Score
0.97
3' ss Seq
GTTTGTTTTTCTTTGTTAAGGAA
3' ss Score
7.04
Exon sequences
Seq C1 exon
TGCCTTCTACTCCTGTGCATCTCACCAATGAGATGAAAAACTACATGAAGAAATCTTCCTACATGCAAGACAGTGCTATAGATTCTTCTTCCAAGGATCACCACTGGTCACGTGGTACCCTGAGGCACATCTCGGAGAACTCCTTTGGGCCATCTGGGGGCCTGCGGGAAGGAAGCCTGAGTTCTCAAGATTCCAGGACTGAGAGTGCCAGCTTGTCTCAAAGCCAGGTCAATGGTTTCTTTGCCAGCCATTTAGGTGACCAAACCTGGCAGGAATCACAGCATGGCAGCCCTTCCCCATCTGTAATATCCAAAGCCACCGAGAAAGAGACTTTCACTGATAGTAACCAAAGCAAAACTAAAAAGCCAGGCATTTCTGATGTAACTGATTACTCAGACCGTGGAGATTCAGACATGGATGAAGCCACTTACTCCAGCAGTCAGGATCATCAAACACCAAAACAG
Seq A exon
GCATAGTTTAATTTTAATATTTTGGTTTTCTCATTTAACAAAGCAAAATAGCAGCAAATAAGTTACAGAGCACAATAATCTACAAGATGCTTTCATTATTCTGGAAAAAAGAAATAGTTTATATCTTCTAATTGCTACTGCATTTGATGCTAACTTTCAGAGAAATCAACAGCTTTGGATAATAACTTTAAATGGCTATGACTTTGCAAACTTGCTATCTAATAACCCAAAGAAGGAATATGCAGATTATGATTGTTTTCTTACCAGTTGTTTGTCTCTGGCATATTTAATGTTTGTATTAATAAGAGAATTTTAATATCTGAAAATTGTTTCTAAATAGTTCGTATAATGGGCATTTGAATTCACTATTTATAGTCTAAATTCTTCTGAAGTTCTGAATGAATGATGATAACGACATTGAAAATAGCTCATTCTGGCTGGGCACAGTGACCCACATCTATAATCCCAACACTTTGGGAAGCAGAGGTGGGAGGATTGCTTGAGGCCAGGAGTTCAAGATCAGCCTGGGCAACATAGGGAGACCCTATCTCTACAAAACATTTCTTAAAAAATTATCCAGGCAAGGTGGCATGTATCTGTAGTCCTAGCTCCTTGGGAGGCTGGGTGGGAGGATCGCTTAAGCCCAGAAGCCCAGGCGATCGAGCCAGACCCTAACAGAAAGAAGGGAAGGAAAGGAGGAAGGGAGGGAGAGAGATAAGGAAGGGAAGAAAGAGAGTAGCTTATTCCTAGAAATGATACAAATTTAAACTCAAATTCACAAGCAGTTTTAGAAAAAAATCTAACGCCTTTTGTTTACTGAAAAATCAACATTCCTTATAAGAGTTATACTCTTATAAATAGGGCTTAGCTGTTGTTCCCATGTTTATATTATTGGATTTATAAATATAAGTAATGTAAACATGAAATCCCATTTTAGAGGCTTGGGTTAAAAGCTACTGCTTGATATATATTGATTATTAAAGGAAATAAAACTAATTTGTAAATTTAGGAATATAAAAAGCATTGGACCAGGATTATATAAAAGCCAGGTTTGAACTGGGTTCTATATAGGTTTCCATCTGCCATATCTAGCAGTTTGACCTGAAGCAAGCTCTTTAATCTCTGGATATCAGTTTCCTCAACCATAAAATATGAATACATTGGACTAGATGATCTCTAAGATCTCTTCCAACCTTTATGTTCTTTGACTATACTCTATCCTTTAATATCTTGCTTTTTCATAATTTTTCCAAAAACACATATTTGTCTTTCAGTAATAATTCATTTTGATTCTAGCCAGCTTTGTCCTGGGCTAGGTTTAAAAAAAAAGAAATTAAAAAAAGAAAAATTATAATTCATTTTGACTCTAACAAGAAATCTTTGTTTGTTTTTCTTTGTTAAG
Seq C2 exon
GAATCTTCCTCTTCAGTGAATACATCCAACAAGATGAATTTTAAAACTTTTTCTTCATCACCTCCTAAGCCTGGAGATATCTTTGAGGTTGAACTGGCTAAAAATGATAACAGCTTGGGGATAAGTGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163629:ENST00000427191:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.968 A=NA C2=0.843
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(18.1=34.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGCCATTTAGGTGACCAA
R:
CGTGACACTTATCCCCAAGCT
Band lengths:
354-1756
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains