HsaINT0114826 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139396724-139397782:-
Coord C1 exon
chr9:139397634-139397782
Coord A exon
chr9:139396941-139397633
Coord C2 exon
chr9:139396724-139396940
Length
693 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
CCTGGCCCCCGTGCCCGCAGGTG
3' ss Score
12.04
Exon sequences
Seq C1 exon
CTCCATCGTCTACCTGGAGATTGACAACCGGCAGTGTGTGCAGGCCTCCTCGCAGTGCTTCCAGAGTGCCACCGACGTGGCCGCATTCCTGGGAGCGCTCGCCTCGCTGGGCAGCCTCAACATCCCCTACAAGATCGAGGCCGTGCAGA
Seq A exon
GTAAGTGTGGCCCCATCCCGGGAACAGGCTCTGCCTGCAGGGGGTGCCATCCCCCCGTGCCCCAGACACGCTGGCTGTTTGTGCCAGTTGCTACCCACGGGTGTGAGCGTTGCCGTCCGAGTTGGGGTAGGGCTTTTCTGGAATTTTCTGAATGGCACTCCGCCCCCACCTGCGGCGGTCACAGCTGCCGGTGGAGCCACCTGGGAACGAGTCCAGCCACGGGAAAGTGGGTGCCTGCTTCTCTCCCCACCCTTTCCTCCTGAATTTTCTTTGTTGGGTATTATTTCAAAATCATTACGGCTTTTTTTAAAGAAAAAAAAAGAGAGAGAGAGAAGAATTGATCGGTGTCATGTGAAGTGTTGAAGTTTGTATCTTGAAAATCCCTCTAAATCCTTTGTCTTAACAGCTCAGTGCGAGTGCAGCGATTTGAAGTTGACTAATCCTCCTTCCTTAAAGGAGAAAAAAGTAAAAGCCGTCTCCAGATAGAGTCGGCTGGTGCAGGAGAGAATTTAGCGATAGTTTGCAATTCTGATTAATCGCGTAGAAAATGACCTTATTTTGGAGGGCGGGATGGAGGAGAGTGGGTGAGGAGGCGCCCGGACGCGGAGCCAGTCCGCCGCCCCCCGGCCACCAGCCTGCTGCGTAGCCGCTGCCTGATGTCCGGGCACCTGCCCCTGGCCCCCGTGCCCGCAG
Seq C2 exon
GTGAGACCGTGGAGCCGCCCCCGCCGGCGCAGCTGCACTTCATGTACGTGGCGGCGGCCGCCTTTGTGCTTCTGTTCTTCGTGGGCTGCGGGGTGCTGCTGTCCCGCAAGCGCCGGCGGCAGCATGGCCAGCTCTGGTTCCCTGAGGGCTTCAAAGTGTCTGAGGCCAGCAAGAAGAAGCGGCGGGAGCCCCTCGGCGAGGACTCCGTGGGCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.260
Domain overlap (PFAM):
C1:
PF076847=NODP=FE(79.4=100)
A:
NA
C2:
PF076847=NODP=PD(14.3=12.3)
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:
GAGATTGACAACCGGCAGTGT
R:
TTGAGGCCCACGGAGTCC
Band lengths:
350-1043
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)