HsaINT0114821 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139401168-139401889:-
Coord C1 exon
chr9:139401757-139401889
Coord A exon
chr9:139401426-139401756
Coord C2 exon
chr9:139401168-139401425
Length
331 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
GACGAAACCTGGCCCCGCAGGTG
3' ss Score
6.19
Exon sequences
Seq C1 exon
TGCGTGGCCGGCTACCACGGGGTGAACTGCTCTGAGGAGATCGACGAGTGCCTCTCCCACCCCTGCCAGAACGGGGGCACCTGCCTCGACCTCCCCAACACCTACAAGTGCTCCTGCCCACGGGGCACTCAGG
Seq A exon
GTAAGGGCCGCTGCACGGAGGGCTGGTGTTGGCCATCCATGGCCAGGGCAGGGGCAGGGCAGGCACCCCGGGACCGGCCAGAGGCATCCAGGAACCAGCCAGAAACTCCCATTTTCCTGTGTGAGGCCAAGGCCGACTCACAGCTGCCCAGGGAAAGGGCCCAGAGCGGGGGTCCCAGTGGGAAGGGCGTCTCCACGGCACCCTTGACACCTGCCTCTCCCGAGTGTCCGTGCAGCCCCAGACCTGAGCGCTCGTCTTCCGGGACGGACACGCGGCACGGCAGGGCCGGGGTGTGGCGGGCTTGGGCCACTGACGAAACCTGGCCCCGCAG
Seq C2 exon
GTGTGCACTGTGAGATCAACGTGGACGACTGCAATCCCCCCGTTGACCCCGTGTCCCGGAGCCCCAAGTGCTTTAACAACGGCACCTGCGTGGACCAGGTGGGCGGCTACAGCTGCACCTGCCCGCCGGGCTTCGTGGGTGAGCGCTGTGAGGGGGATGTCAACGAGTGCCTGTCCAATCCCTGCGACGCCCGTGGCACCCAGAACTGCGTGCAGCGCGTCAATGACTTCCACTGCGAGTGCCGTGCTGGTCACACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:22
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(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
A:
NA
C2:
PF0000822=EGF=PD(6.5=2.3),PF0000822=EGF=WD(100=44.8),PF0000822=EGF=PU(90.9=34.5)
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:
TGCTCTGAGGAGATCGACGAG
R:
TCGCAGTGGAAGTCATTGACG
Band lengths:
344-675
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)