HsaINT0114814 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139405105-139405723:-
Coord C1 exon
chr9:139405604-139405723
Coord A exon
chr9:139405258-139405603
Coord C2 exon
chr9:139405105-139405257
Length
346 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GGCCTCCTCCTGCCCCGCAGGGC
3' ss Score
9.93
Exon sequences
Seq C1 exon
GTGCCACGTGTGAGGTGGTGCTGGCCCCGTGTGCCCCCAGCCCCTGCAGAAACGGCGGGGAGTGCAGGCAATCCGAGGACTATGAGAGCTTCTCCTGTGTCTGCCCCACGGGCTGGCAAG
Seq A exon
GTGAGGCTGGCCAGGGCCCGGTGAGGGCTGGGATGGGAGGTCAGGATGTCTGCGGGACACAGGCAGCTCCCAGGCAGGCTAGATGAGTCTTTGAAGAGGAGCTGGTGGGTGCTGAGGAGGCCCTGGTCGGAGAAGTTCTGGAATCAGGAATTGACCTGGGAGCACCGTTCCCAACTCCAGTTCCTGTGACCTTCTTAGGCCAAAATTAGGGGAGAGGGGATGGTCCTGGGGTCACGGAAGCCTACTCCTGGGTCGGGAGAGGCACTGTAGGTGGGTGGGCCAGCCTGGGAAGGGCCTGGAGGGCCAGGGGCCGCTGGTGACCAACCGGCCTCCTCCTGCCCCGCAG
Seq C2 exon
GGCAGACCTGTGAGGTCGACATCAACGAGTGCGTTCTGAGCCCGTGCCGGCACGGCGCATCCTGCCAGAACACCCACGGCGGCTACCGCTGCCACTGCCAGGCCGGCTACAGTGGGCGCAACTGCGAGACCGACATCGACGACTGCCGGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:16
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=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0764510=EGF_CA=WD(100=73.1),PF0000822=EGF=PU(9.7=5.8)
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:
CACGTGTGAGGTGGTGCTG
R:
GCAGTCGTCGATGTCGGTC
Band lengths:
262-608
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)