HsaINT0114898 @ hg19
Intron Retention
Gene
ENSG00000074181 | NOTCH3
Description
notch 3 [Source:HGNC Symbol;Acc:7883]
Coordinates
chr19:15276598-15278222:-
Coord C1 exon
chr19:15278060-15278222
Coord A exon
chr19:15276903-15278059
Coord C2 exon
chr19:15276598-15276902
Length
1157 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
ACACACTCCTGTCCCTGCAGATG
3' ss Score
10.8
Exon sequences
Seq C1 exon
GTAGAGGAGCCAGGCATGGGGGCTGAGGAGGCTGTGGATTGCCGTCAGTGGACTCAACACCATCTGGTTGCTGCTGACATCCGCGTGGCACCAGCCATGGCACTGACACCACCACAGGGCGACGCAGATGCTGATGGCATGGATGTCAATGTGCGTGGCCCAG
Seq A exon
GTTAGTGACAGTGCCCCTCCCAAAGGGATGCCCCTCACCCATCCTACCTGTGAGAGGTTATTTCTGACTCTGTGTTTTGGGGAGAACTGGGGGAGTCTCTAAGCTTCTGTGAAGGGTGTGTGTATTCAGCAACACTCTTGGTTGGAAGTGACAAAGGTCCAACTCAGACTAGCTTAAGTAAAACAAGGGATTTATCAACTCATTTAACTAAAAGTGGCACATTTGGATCCAGGACTCAGTTTTCCCCTCTCTACCCTTTGACTCCAATCTTACAAAACCTTCTTAATGCTCCAGAAAAGTCTCAGGATGCATTCTGATTGGACAGACTAGGGTCACGTGCTCATCCTTGAGCCAATCAGTATGACCAGGGGGCTGGAATATGCAAATTGACCAAGCCTGATTCACATACCTGTCTTTGAGCTGGTGGGGGTCGGGTCTGCTGGTGGAGCGGGGAGGTCAGTCTCTACCCAGGGCTTGAGAATGGAGAACCGGATGCAAGTGGCTCCCTAAGAAAAATGAGGACAAGTGCTTGTGTACAGTGTGTGCAGTGTAGCGGACTATGTTGTTTGATCCTCTTAGATCCATCTTTGTTATGTTTCAGGGCATTCCTGCCTTAGCTTCATTTTGCTTATGCTCCAAATGGCCTGTACTTATGGCTCTCTTTTGAAGTCCCTCTGGCTGCTGGGGCCTGAAGTGCCTGGGATTTTATGTCCCTGGGGGCAGCTCTTTTTTTCCCCCCCCCTTTTAAAACACTCAAATGAATTGGCAGAAAGGGGCAGCTCCTAACCAGTGGGTGCAGGAGTATGAAGGGGATGGTTTCTTTGCCTTGAGTTGGATTAGAACTCTGGGGTACAACACATGTTCCAGAGTCCCTTTGGAGGATCAAGGTGGAATAACCCTTTGGGAATTTACTGGAGGTTGCACACTTGCTTGACTCCCAGAGTCCCTTGTCCTGTGTTCCCTGTGCCCTAGGAGTAGTTCTGTGACAAATCACGTGCCCACGAATCCTCATTCTGGGTGTGGGTGTGCAGACAGGAGGATCTGCTAATTGTCATTTTTCCATGTGTCCCATTAGCTCCTAATGGGGTACCCTTGATAACATTTCCTGGAAAAGGCCCTGTGTTTACCTTCCTGCTGACACACTCCTGTCCCTGCAG
Seq C2 exon
ATGGCTTCACCCCGCTAATGCTGGCTTCCTTCTGTGGGGGGGCTCTGGAGCCAATGCCAACTGAAGAGGATGAGGCAGATGACACATCAGCTAGCATCATCTCCGACCTGATCTGCCAGGGGGCTCAGCTTGGGGCACGGACTGACCGTACTGGCGAGACTGCTTTGCACCTGGCTGCCCGTTATGCCCGTGCTGATGCAGCCAAGCGGCTGCTGGATGCTGGGGCAGACACCAATGCCCAGGACCACTCAGGCCGCACTCCCCTGCACACAGCTGTCACAGCCGATGCCCAGGGTGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000074181-NOTCH3:NM_000435:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.636 A=NA C2=0.392
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF127962=Ank_2=PU(83.5=74.5)
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:
CCATCTGGTTGCTGCTGACAT
R:
GTCCTGGGCATTGGTGTCTG
Band lengths:
349-1506
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)