HsaINT0114810 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139408962-139409852:-
Coord C1 exon
chr9:139409742-139409852
Coord A exon
chr9:139409155-139409741
Coord C2 exon
chr9:139408962-139409154
Length
587 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTGACCCGCCCTGCCCTTAGGGA
3' ss Score
10.51
Exon sequences
Seq C1 exon
GACCCAACTGCGAGATCAACCTGGATGACTGTGCCAGCAGCCCCTGCGACTCGGGCACCTGTCTGGACAAGATCGATGGCTACGAGTGTGCCTGTGAGCCGGGCTACACAG
Seq A exon
GTGAGCGGCCCTGCACGTGGGGGCTGACTGCACTGTGCTCAGAGGTCAAGGTCAGCCACTCTGCCCTGGGGCTGCTGAGGGGTTGGGTGAGGGCTTTGGTGCTGCCCACCTGGGCAGACCGTGGTCTGCAGCAGAGATTGCAGCGGGACCAGGGCTATAACTGGCAGCACGATGGGTCCCCCCGACCCCTCTTGTCTCCGGTCAGAGCTGTCCCAGGCCGTGTTGGCAGAGTGGCCCAGCAGGCCAAGAGGGAGCAGCCAGCCCTGAGGCCAGGCTTAAGTACCTTCTGCCTCTGTGGCTCACCAGCACCTTTGAGCAGGTCCCTCTGCCTCTCTGGGCCTCAGATTCTCATCAGTCAGGGCTGCAGTAGCCCCTGCCCCTGGGGCCCCTGGGAGGATGACTTGAGTGGGCACTGGTGCCCGGGGAGGCTGGCACATGGCACATTGTGATCCAAGATGGTTTCTGACACCTGGAAGGATGTGGCCAGAAGGGTGATCGCCCCGGCTCAACAGACAGGGAAATCGAGGTTGACGTGGGTGGGACCCCCTGGGCGCTGGGCCTCGGAGTCTGACCCGCCCTGCCCTTAG
Seq C2 exon
GGAGCATGTGTAACATCAACATCGATGAGTGTGCGGGCAACCCCTGCCACAACGGGGGCACCTGCGAGGACGGCATCAATGGCTTCACCTGCCGCTGCCCCGAGGGCTACCACGACCCCACCTGCCTGTCTGAGGTCAATGAGTGCAACAGCAACCCCTGCGTCCACGGGGCCTGCCGGGACAGCCTCAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:12
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=5.3),PF0000822=EGF=PU(93.1=71.1)
A:
NA
C2:
PF0000822=EGF=PD(3.4=1.5),PF0000822=EGF=WD(100=58.5),PF0000822=EGF=PU(53.3=24.6)
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:
GACCCAACTGCGAGATCAACC
R:
GTTGAGGCTGTCCCGGCA
Band lengths:
302-889
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)