HsaINT0114879 @ hg19
Intron Retention
Gene
ENSG00000074181 | NOTCH3
Description
notch 3 [Source:HGNC Symbol;Acc:7883]
Coordinates
chr19:15297689-15298149:-
Coord C1 exon
chr19:15297916-15298149
Coord A exon
chr19:15297800-15297915
Coord C2 exon
chr19:15297689-15297799
Length
116 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
GCCATGTTCCTGGCCCCTAGGTG
3' ss Score
10.2
Exon sequences
Seq C1 exon
GCTTTGAGGGCACGCTGTGTGATCGCAACGTGGACGACTGCTCCCCTGACCCATGCCACCATGGTCGCTGCGTGGATGGCATCGCCAGCTTCTCATGTGCCTGTGCTCCTGGCTACACGGGCACACGCTGCGAGAGCCAGGTGGACGAATGCCGCAGCCAGCCCTGCCGCCATGGCGGCAAATGCCTAGACCTGGTGGACAAGTACCTCTGCCGCTGCCCTTCTGGGACCACAG
Seq A exon
GTGGGACCGGGGGCTGGGGCAGAAACAGCACACCTGGAGGGGCACAGAGGGTTTGGGAATGGTGCATCTAGTGGGGCACAGTGGTGGCCACTCCATGCCATGTTCCTGGCCCCTAG
Seq C2 exon
GTGTGAACTGCGAAGTGAACATTGACGACTGTGCCAGCAACCCCTGCACCTTTGGAGTCTGCCGTGATGGCATCAACCGCTACGACTGTGTCTGCCAACCTGGCTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000074181-NOTCH3:NM_000435:11
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(16.1=6.3),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(90.0=71.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCTCATGTGCCTGTGCTCC
R:
GGTTGGCAGACACAGTCGTAG
Band lengths:
246-362
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)