HsaINT0114892 @ hg19
Intron Retention
Gene
ENSG00000074181 | NOTCH3
Description
notch 3 [Source:HGNC Symbol;Acc:7883]
Coordinates
chr19:15288336-15289752:-
Coord C1 exon
chr19:15289634-15289752
Coord A exon
chr19:15288902-15289633
Coord C2 exon
chr19:15288336-15288901
Length
732 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TCCCCAAACCCGACCCCCAGCCG
3' ss Score
3.88
Exon sequences
Seq C1 exon
GTCCTCGCTGTCAGACTGTCCTGTCTCCCTGCGAGTCCCAGCCATGCCAGCATGGAGGCCAGTGCCGTCCTAGCCCGGGTCCTGGGGGTGGGCTGACCTTCACCTGTCACTGTGCCCAG
Seq A exon
GTAGGTGTGGGTGGCGGCCTTTGGAGGAGGAGTAGGGGCGTGGCCTCTGGAGTAGTAGGGGCGTGGCGTCTAGGAGGAGGATGTGGCTTTAGGGGAGACATCGAAGGGAAGGGAGTTTCTGGAAAATGCTGACATTTCCGCCGGGTGTGGTAGCTCACACCTGTAATCCCAGCACATTGGGAGGCCGAGGCGGGAGGATCACTTGAGGCCAGGAGTTAGAGACCAGCCTGGGCAACATGGTGAAACCCCGTCTCTACTAAAAATATAAAAATTAGCCGGGCGTAGTGGCAGCTGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCATCACGCCATTGCACTCCAGCCTGGCGACTGAGTGACACTCCGTCTCAAAAAACAAAGAAACAACCCCCTGCCCCGACATTTCCTGGAGGTTTGAAGGGAAAAGGGTGAGGATGGTGATTGGGGGGCGTGGCCTCCTGGGATGGCAGGGCTTATCTGCCAGGTGGGGTCTCCAGTGTGGAAAGGGGAGCGGTTGGGTGGGACATGGGGAGGTTGAGGGGGTCTCAACCTTCCTTAGTCTTGACCTCTTCTCTTCCCCCTCTCTCCCCTTGACTCTTCTTTTCCCCACTCCTCCATTTCTTCTCCTCCTTCCCTCCACTCCCCACCCTCATTTTTATCCCTCCCTCCCCAAACCCGACCCCCAG
Seq C2 exon
CCGTTCTGGGGTCCGCGTTGCGAGCGGGTGGCGCGCTCCTGCCGGGAGCTGCAGTGCCCGGTGGGCGTCCCATGCCAGCAGACGCCCCGCGGGCCGCGCTGCGCCTGCCCCCCAGGGTTGTCGGGACCCTCCTGCCGCAGCTTCCCGGGGTCGCCGCCGGGGGCCAGCAACGCCAGCTGCGCGGCCGCCCCCTGTCTCCACGGGGGCTCCTGCCGCCCCGCGCCGCTCGCGCCCTTCTTCCGCTGCGCTTGCGCGCAGGGCTGGACCGGGCCGCGCTGCGAGGCGCCCGCCGCGGCACCCGAGGTCTCGGAGGAGCCGCGGTGCCCGCGCGCCGCCTGCCAGGCCAAGCGCGGGGACCAGCGCTGCGACCGCGAGTGCAACAGCCCAGGCTGCGGCTGGGACGGCGGCGACTGCTCGCTGAGCGTGGGCGACCCCTGGCGGCAATGCGAGGCGCTGCAGTGCTGGCGCCTCTTCAACAACAGCCGCTGCGACCCCGCCTGCAGCTCGCCCGCCTGCCTCTACGACAACTTCGACTGCCACGCCGGTGGCCGCGAGCGCACTTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000074181-NOTCH3:NM_000435:23
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:
PF0764510=EGF_CA=PD(29.4=37.5),PF0000822=EGF=PU(80.6=72.5)
A:
NA
C2:
PF0000822=EGF=PD(13.9=2.6),PF0000822=EGF=WD(100=17.5),PF0006612=Notch=WD(100=19.6),PF0006612=Notch=WD(100=19.6),PF0006612=Notch=PU(15.0=3.2)
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:
TCCTCGCTGTCAGACTGTCC
R:
GAGCCCCCGTGGAGACAG
Band lengths:
327-1059
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)