HsaINT0114830 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139395004-139396365:-
Coord C1 exon
chr9:139396200-139396365
Coord A exon
chr9:139395300-139396199
Coord C2 exon
chr9:139395004-139395299
Length
900 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
ACCCGTCTCTGCCTCTGCAGATG
3' ss Score
11.67
Exon sequences
Seq C1 exon
TTCGAGGAGCCCGTGGTTCTGCCTGACCTGGACGACCAGACAGACCACCGGCAGTGGACTCAGCAGCACCTGGATGCCGCTGACCTGCGCATGTCTGCCATGGCCCCCACACCGCCCCAGGGTGAGGTTGACGCCGACTGCATGGACGTCAATGTCCGCGGGCCTG
Seq A exon
GTAAGGGTGCCAGCAGCCAGGGCTTCCCTAGCCCCGTGGCCCACCTGCCTCTCTCCCCTAAGCCCCGAGGCTGGGGTACAGTTGATACTCTGGAAACTTAGAATTGGGGGTGAGAGCTTTCATCCTTGGGGTGTTTCCCATTCAGAGTAGACGTGGGGGGGTCCTGGAGTCCTCCTGTTCTTCCACCAACCCCTTCCTGGGGTGATACCGCAGGGCCACTCTGTCCCTGTAAATTACTCTTTTCTGAAACCTTCTTGAGACATGGAAAGCGTTGATTTTCTTTTTCTTTTTTTTTTTCTTTTTTTTTTGTTTTTGAGATGGAGTCTCGCTCCGTCACCCAGGCTGGAGTGCAGTGGCACGATCTCGGCTCCCTGCAACCTCCACCTCTCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCCAGTAGCTGGGACTACAGGCGCCTGCCACCACACCTGGCTAATTTTTGTATTTTTAGCAGCGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCACCTCGGCCTCCCCCAGTGCTAGGATGACAGCGTGAGCCTCCGCATCCTGCTGAAGCATTAATTTTCTAACTGCATGCTTCTGGGGTCCTCTTTTTCCTGGGTGGATTTTGGGTGCCAGGTCTTGGGCAGGTCAGGAAGCAGTTGCCCGCCAGGAGTTTAAGCTGGATTCGGCTCTGTCCACTGAGCAGCCCAGGCGGACTTCAGCTGCCCCTTGGTGGCTGTGTGCACGGGGCCACCAAGTGCTGGGTGGTGCATCCACACCGTGGCCCCTTGAGCTTGGGGCTGCTGCCCCCCTCCCCCTGGGCTGCAGCTGGGGACCGGCCCTCCAGACTGAGCACCCGTCTCTGCCTCTGCAG
Seq C2 exon
ATGGCTTCACCCCGCTCATGATCGCCTCCTGCAGCGGGGGCGGCCTGGAGACGGGCAACAGCGAGGAAGAGGAGGACGCGCCGGCCGTCATCTCCGACTTCATCTACCAGGGCGCCAGCCTGCACAACCAGACAGACCGCACGGGCGAGACCGCCTTGCACCTGGCCGCCCGCTACTCACGCTCTGATGCCGCCAAGCGCCTGCTGGAGGCCAGCGCAGATGCCAACATCCAGGACAACATGGGCCGCACCCCGCTGCATGCGGCTGTGTCTGCCGACGCACAAGGTGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.821 A=NA C2=0.424
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF127962=Ank_2=PU(84.3=75.8)
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:
GACTCAGCAGCACCTGGATG
R:
GCCCATGTTGTCCTGGATGTT
Band lengths:
355-1255
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)