HsaINT0114827 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139396453-139396940:-
Coord C1 exon
chr9:139396724-139396940
Coord A exon
chr9:139396541-139396723
Coord C2 exon
chr9:139396453-139396540
Length
183 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGC
5' ss Score
6.39
3' ss Seq
CTCGACCCCTCACCCCCCAGGCC
3' ss Score
8.93
Exon sequences
Seq C1 exon
GTGAGACCGTGGAGCCGCCCCCGCCGGCGCAGCTGCACTTCATGTACGTGGCGGCGGCCGCCTTTGTGCTTCTGTTCTTCGTGGGCTGCGGGGTGCTGCTGTCCCGCAAGCGCCGGCGGCAGCATGGCCAGCTCTGGTTCCCTGAGGGCTTCAAAGTGTCTGAGGCCAGCAAGAAGAAGCGGCGGGAGCCCCTCGGCGAGGACTCCGTGGGCCTCAA
Seq A exon
GTGAGCGGACGCCGCCCCTGCTTCTGGGTCCCCGGTGGGAGGTGGGACCTGGCCGAGCATCCTCACCGGGAGTCTGCCCCTCCCGACCCAGGGCCCACCTCCCACGCCAGGCCCGGGCCAGGGGTCTCTGGGGGCTTCCTAGGGAGCTCGCTCAGCCTCACTTCTCGACCCCTCACCCCCCAG
Seq C2 exon
GCCCCTGAAGAACGCTTCAGACGGTGCCCTCATGGACGACAACCAGAATGAGTGGGGGGACGAGGACCTGGAGACCAAGAAGTTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.260 A=NA C2=0.733
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(14.3=12.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGCACTTCATGTACGTGG
R:
CCCCACTCATTCTGGTTGTCG
Band lengths:
244-427
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)