HsaINT0114807 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139438476-139440238:-
Coord C1 exon
chr9:139440178-139440238
Coord A exon
chr9:139438555-139440177
Coord C2 exon
chr9:139438476-139438554
Length
1623 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
CTTCTCCTGCCCCTGCCTAGGCC
3' ss Score
9.24
Exon sequences
Seq C1 exon
ATGCCGCCGCTCCTGGCGCCCCTGCTCTGCCTGGCGCTGCTGCCCGCGCTCGCCGCACGAG
Seq A exon
GTAGGCGCCCACCCACCCGCGAGCCCCCACTTTCCGCGCCCTTTGGAAACTTTGGCGGCGCCCGGCGCGCGCGCCCCACGGCTGGGAGCGGGCGGCGGGGAGGCCAGCATGGAGAGGGAAAAGCGGGCGGCCCGGGGCGTGGGGTTCTGGAGTCCCGGGATCAGGGAGGACCGACCTTCCCCCTCGATCCCCCCGTGGAGGCGGACTCGCGCCGCCCGTGCCTGGAGCCGAGTTAGGAGGCCGGTGTGGGGTGCTGGGGCCCCGGAGGCCCTACTCCGGGCCCGCCCTTCACCCGCCGCGCGTGGGGCTTGCCGCCGGTCGGCCGGGCGGGCGGGCTGCCTACTATTTTTCGATTTGAATAGAGTCGGTTTTGGTTTCCTGTTGCTTCTCCGGGCCATTTATCTTCTTTCTTCTTCGCCTCTGGCCCACGCCGGGGCGGATGTTGGGGCGCGGAGTGTGGGCTCTGCGGCGCCGCGTTCGCCTTCACTGACCCGCGCGGCCGGGCTGGGTCCCCGGGCTCCCGGTCGCCCCGCCCGCCGGTGCCCCCCAGCCCGGCTCTCAGTTTGGGGGAGGGGTTGCGTAAGAAGCCGCCGCGCCCGGGGGGACTGAACTTTCCTTTTGCTTTGCGGAGTTGAAGTTTGGAAAGCTTGGGGGCGGAGAGCGGGACGCGGGTGGGGGGCTCTTACATTTCTCCCCGCCGCACAGCGAGCGGGGTCTCTGGGGAATCGAGTGATTAATCCACTCTTTCTCCGAGAGTTGGAGGCGAGAATTATCTGTCCTCTTCCAGAAAGTGCGGCTCTGTGTCACACCCCCCTCCCCCGTTTCTCAGCCCCGGTAAGATGGGGAGGGAGGGGCTTGAGTAATTGATCCCTTCTCGAGATGGGGTCGAATTCCTTCCGAATGGGGGACCTTCATCCCCCTCCTGTGGGTGTATGGGGGCTGCCCTGGAGATGCGCGCCCGCGGAGGCAGGTATTGGGTGTCGGCGGAGGCGGGGCCGCGTCCCCAGGGTGCTGTCCCGGTGCCCCTGGAGGCGGCCCCGACTCCACAATGGGCCGCTCTGATTCTGAGGCGGAGGCCGGCGCTTTGTTGGCGGGCGGGGTAGCGGGCGAGCAGCTGTCGCATTTTCCCACGGGCGGGAGCTGAGTGTGGCCACCCCCCCTCCCCCCGTCCAGCTCTGCCCCCTTGCAGAACGGGTTTGAACAGAGGCAATCTCGGCGGCTGGATGGGGGGCCCTGCCCTGCCAGACTCCTCAGTGAGCCTCCAGGGTGGGGGGCAACGCTTTGGAGAGTAGCCCACTTTGTCTCTGCTTTTCCCCCACTGCGTCCAGGCGGCACATCAGGCCACCCCACCCTGCTTCAAGCAGGACGTGTTCCCTGCTGCTCCCCTTCCCCCCATTTCTGACTACAGAACTCTGGGCAGAATGTTGACGCCCCTTTGGTTTCATGGAGGGGCTTCCTGCGGACCCGTGCCCCAGCAACCCATGATACTGAGCAGAGTGCGTCCGGGGTAGGGGGCGGACGATGCCCCTTGGCTGGGTGCAGGTCCCCGCCCCCAGGGTAACCAGGGCCTTCGGTGGTGGTGGTGCGGGTGAGACTGACCTCTCTTCTCCTGCCCCTGCCTAG
Seq C2 exon
GCCCGCGATGCTCCCAGCCCGGTGAGACCTGCCTGAATGGCGGGAAGTGTGAAGCGGCCAATGGCACGGAGGCCTGCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)