HsaINT0134337 @ hg38
Intron Retention
Gene
ENSG00000163629 | PTPN13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:HGNC Symbol;Acc:HGNC:9646]
Coordinates
chr4:86732592-86734456:+
Coord C1 exon
chr4:86732592-86732766
Coord A exon
chr4:86732767-86734302
Coord C2 exon
chr4:86734303-86734456
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:ENST00000427191:12
Average complexity
IR
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