HsaINT0173485 @ hg19
Intron Retention
Gene
ENSG00000165699 | TSC1
Description
tuberous sclerosis 1 [Source:HGNC Symbol;Acc:12362]
Coordinates
chr9:135777992-135779204:-
Coord C1 exon
chr9:135779038-135779204
Coord A exon
chr9:135778175-135779037
Coord C2 exon
chr9:135777992-135778174
Length
863 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
ACATTTCTGGTCTCTGCTAGAAA
3' ss Score
6.52
Exon sequences
Seq C1 exon
GCTCTCCTCCTTCAGATGAGATCCGCACCCTCCGAGACCAGTTGCTTTTACTGCACAACCAGTTACTCTATGAGCGTTTTAAGAGGCAGCAGCATGCCCTCCGGAACAGGCGGCTCCTCCGCAAGGTGATCAAAGCAGCAGCTCTGGAGGAACATAATGCTGCCATG
Seq A exon
GTGAGGACTGGGGAGGGGACAGGTGGAGCTTGCTTTTTGTTTTGTTTTGGGTCAGCATGATAGCTTATAAAGCACAGCAGCCGAGGAGGTCAGAGTTCCCAGTCCTTCCCACTCCTTTGGGCAGGTCGCTTGAGATTAAGACATGAATGGTGACACCTCGGAATTCCCTCATAATTCTCAGAAACCGTGGGGACAAGTGATTTTGTGTGTGTATGTTTGCATGTAACTGGCCATGATGATGAAGGGTCAGAAGATGATTTTATTTCTCCAAATGTAAAACCAACTCTTGTAAAGCTATTTCATGGCACAAAACTGAAGCGTGTATTGTACAGCGGGTGTGAAGCCAGTCAGGCCTGGAGTTTGAATCTTGGCTCTACCAGTGTTACCTTAGAAAAGTAACGTGGCCTCTTGAAGCCTCTGTTAGCCATGCTATAAAATGGAAATAACAATAGCAGCACCTGCTCTTTAAGTTGTGATGGTTAAAAGAAATTATGTCGGTAAGCCCTTGCTGAGCGCCCAGCACACTGCAAGCATTCAGTAAATGCTCATCGTTTCAGTGAACTTAGTACCATGTTTGAGAGATTTTATTCCAGTGTTGGTAGTCAGACTTTTGAAAGTATTGGAAGCAAACTGATCCCTGAGAAGATTTATTTAAGCAACTTAAGATCCATTTGCTTAATGTAAAATTTGGAAAACCTTGACCTAAGGCCAAGTAAGACAGTAGTGAGCTCTAAGAGTTTTGGTCTGTAGTTAGTTACATTTTCAGGGTAGCTTATGACTATTCAGATGAAATGTTCGCAGTGTGTGTTAAATTGCCTGTGTTGGAAGACAGCTAAAATGATGACATTTCTGGTCTCTGCTAG
Seq C2 exon
AAAGATCAGTTGAAGTTACAAGAGAAGGACATCCAGATGTGGAAGGTTAGTCTGCAGAAAGAACAAGCTAGATACAATCAGCTCCAGGAGCAGCGTGACACTATGGTAACCAAGCTCCACAGCCAGATCAGACAGCTGCAGCATGACCGAGAGGAATTCTACAACCAGAGCCAGGAATTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165699-TSC1:NM_001162427:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.213
Domain overlap (PFAM):
C1:
PF043887=Hamartin=PD(5.3=67.9)
A:
NA
C2:
NO
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:
CCTTCAGATGAGATCCGCACC
R:
CTGTAATTCCTGGCTCTGGTTGT
Band lengths:
342-1205
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)