HsaINT0114822 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139400979-139401425:-
Coord C1 exon
chr9:139401168-139401425
Coord A exon
chr9:139401092-139401167
Coord C2 exon
chr9:139400979-139401091
Length
76 bp
Sequences
Splice sites
5' ss Seq
CCGGTGGGT
5' ss Score
7.85
3' ss Seq
TGCCCTGCTCTTACCCCTAGGGC
3' ss Score
12.39
Exon sequences
Seq C1 exon
GTGTGCACTGTGAGATCAACGTGGACGACTGCAATCCCCCCGTTGACCCCGTGTCCCGGAGCCCCAAGTGCTTTAACAACGGCACCTGCGTGGACCAGGTGGGCGGCTACAGCTGCACCTGCCCGCCGGGCTTCGTGGGTGAGCGCTGTGAGGGGGATGTCAACGAGTGCCTGTCCAATCCCTGCGACGCCCGTGGCACCCAGAACTGCGTGCAGCGCGTCAATGACTTCCACTGCGAGTGCCGTGCTGGTCACACCG
Seq A exon
GTGGGTGCCGCGCCCAGGCGGGTGGGGCGTGTGGGGCAGCAGGGTGAGCCTCTCACTGCCCTGCTCTTACCCCTAG
Seq C2 exon
GGCGCCGCTGCGAGTCCGTCATCAATGGCTGCAAAGGCAAGCCCTGCAAGAATGGGGGCACCTGCGCCGTGGCCTCCAACACCGCCCGCGGGTTCATCTGCAAGTGCCCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:23
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(6.5=2.3),PF0000822=EGF=WD(100=44.8),PF0000822=EGF=PU(90.9=34.5)
A:
NA
C2:
PF0000822=EGF=PD(6.1=5.3),PF0000822=EGF=PU(79.4=71.1)
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:
TGAGGGGGATGTCAACGAGTG
R:
CCCCATTCTTGCAGGGCTTG
Band lengths:
167-243
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)