HsaINT0114831 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139393564-139395299:-
Coord C1 exon
chr9:139395004-139395299
Coord A exon
chr9:139393712-139395003
Coord C2 exon
chr9:139393564-139393711
Length
1292 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
AGCCTCTCCCTGTTGCCCAGATC
3' ss Score
4.6
Exon sequences
Seq C1 exon
ATGGCTTCACCCCGCTCATGATCGCCTCCTGCAGCGGGGGCGGCCTGGAGACGGGCAACAGCGAGGAAGAGGAGGACGCGCCGGCCGTCATCTCCGACTTCATCTACCAGGGCGCCAGCCTGCACAACCAGACAGACCGCACGGGCGAGACCGCCTTGCACCTGGCCGCCCGCTACTCACGCTCTGATGCCGCCAAGCGCCTGCTGGAGGCCAGCGCAGATGCCAACATCCAGGACAACATGGGCCGCACCCCGCTGCATGCGGCTGTGTCTGCCGACGCACAAGGTGTCTTCCAG
Seq A exon
GTAGGCAGTGGCTGCCTGTGTGCCCACCTGCCCTCCTCAGGGCCGCCTGGTGGTCTGGGGCAGTGGCCAGGCTTACGTGGCCCTGGGAGCCTGACCCCGAGCACAGCTGAGTCCGGGACAACTGGTGCCTCCACCTGGGACCTTCGCAGTCAGCGAGGTGCGAGGGGGAGGGCGTCGGGCCCATCTGTGTTCTCCAGGGAAGTCAGGCAGAGGCGGGTCTGGCAGGAGGCCTGGGGGATCTGCTGAGTGAGGCAGCACCTCCCCACCCCCAGCAAAACAGGCTCCATCAGGGTTGTGGGCCTTGCTCAAGGTCCAGGTTCCACTGCTGCAGCCCCTCGCAGCCCCGCCCCTCCCTCAACCTTGGCTGCCGGCGTAGCCTGTGGCAGTGAGAAGCAGGGTTTAGAGGCTGCCGCTCGGTGCCTGCAGACCTAGGGCTCAGCTTGCCGGTGAGCTCGTGGCAAGAATGGATTTAGGGATTTGGATGCCTGGGTCTCCAGGGAGTGTCCCTGGCAGGGGCTGCCTTTGCAGTCACCCCTGCTGCGAGTCCCCAGGCTCCAGGCGGCCCTGGAGCAAGCAGGTTCAGATGGGCACAGCCCGGGGAGTTACCACAGAGCTTCTCATTTCCTGATTTCTTAGCTCAGGTGACACATTGTCATCTCGCAGAAATAAATGTAGGTGAGCAGAAAGAGCGTGGAAGGGAGCCCCGTGCGGGTTTGGTGTGTGCCTCTCTCAGCTGCCTTCTTTGCACAGATGTGGAAGTTCCCAGGTGCTTTGCAGGAATCAGGCCAAGTTGCCTTTTGCACCCGCCAGTGAGCAGGGGCCATTCCTCCTGCCAGATGCCAAGACCCGGCTGCATTACAAGGGCTGCCCACCCCCTCTCTGGGCAGAGCCGGACACTAGCTCGGCGGTTCTGAGACGGCTGTAGGGCCGTGAGCCCGGCTTCCTGAGTGCCAGCTGTAACCGCCGTTGGGGGCAGGGACTTGACCTCTCTGTTTTGTAGGTGGTCATGGCAGCTAGGACCACAGTGAGGATTAAATGAGGCCACACGTGGTCACGATGGATCCCACTGTCACCAAGGGGCCTGTCTGTGGGCAGCACAGCCCCTGCCCCCATCCGGGCCCCTCCTCAGGGGCAGCCCCATGGCGTTTCGTCTTGCCCGGCCGTGCCGATCTCAGGAGGGTCTCGTCTGTGTCCGGAAGACAGTGGGGCTTCCCGTCCAGGCGTTCGTTCTGGGCAGGAGGCATCGGTGTACGTCTGCCCAGCACCCGCCTGAGCCTCTCCCTGTTGCCCAG
Seq C2 exon
ATCCTGATCCGGAACCGAGCCACAGACCTGGATGCCCGCATGCATGATGGCACGACGCCACTGATCCTGGCTGCCCGCCTGGCCGTGGAGGGCATGCTGGAGGACCTCATCAACTCACACGCCGACGTCAACGCCGTAGATGACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:31
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.424 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(84.3=75.8)
A:
NA
C2:
PF127962=Ank_2=PD(13.5=24.0),PF127962=Ank_2=PU(31.2=58.0)
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:
TCCGACTTCATCTACCAGGGC
R:
CAGGTCATCTACGGCGTTGAC
Band lengths:
351-1643
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)