HsaINT0114811 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139407844-139409154:-
Coord C1 exon
chr9:139408962-139409154
Coord A exon
chr9:139407990-139408961
Coord C2 exon
chr9:139407844-139407989
Length
972 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGC
5' ss Score
7.73
3' ss Seq
CAGTGTGGTCCCCCTTGCAGGTA
3' ss Score
10.08
Exon sequences
Seq C1 exon
GGAGCATGTGTAACATCAACATCGATGAGTGTGCGGGCAACCCCTGCCACAACGGGGGCACCTGCGAGGACGGCATCAATGGCTTCACCTGCCGCTGCCCCGAGGGCTACCACGACCCCACCTGCCTGTCTGAGGTCAATGAGTGCAACAGCAACCCCTGCGTCCACGGGGCCTGCCGGGACAGCCTCAACGG
Seq A exon
GTATGCGGCGGGGCCGATCATGGGGACACATCAGTCCTAAACCCTGGGAGCTCTGCTGCCAGGAGGGTGGCACCTGCACAGAGCTTGAGATGGGCCAGAAACGGGCCTCGGACGGGGCTGGGTGGCAGGGAGCTCCCCTCGGGGACGCACATGCCTCTGGGTCCTCAGTCAGACTACAGTCCACACCCAGCAGCTGTGTGCTGCGTGTCCTTGTGGGCTGCATGGTGTGCTCAGGACACAGGCCCACAGTGACCCTGGAACACGTTTCCATGGTAACAGCCGCAAGTGTTTCTGATGCCCATGATGTGCCTGGCAGCACTCTGCCTGGATGGGACCATTTAAATCAGCAGGGACCCCATTGCCCTCATTTGGCGCAGAGAAGGCACGTGCTTTGTTCGGGGCCACACAGCGGGCAAGTGGTGGGGGGCTTTTCGCAGCACCCTACTGCCCTGCACTTGGCATGGTCCCCTCGCTAATGAACCAAACCCCTGCCGCAGTCTTGGGTATGGGAAGCGCTGCGGCCCCCACTTTTTTCTTTATTTTGAGACAGAGCCTTGCTCTGTTGTCCAGGCTGGAGTGCAATGGCATGATCTCAGCTCACTGCAACCTCCACCCCTCAGGTTCAAGTGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGAGATTACAGGCATGTGCCACCACACCTGGCTAATTTTTGTATTTTTAGTATATATGGGGTGGGGGAGTTTCGCCATGTTGGCCAGGCTGATCTTGAACTCCTGGCCTCAAGTGACTCAGCCACCCCCGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACAGCGCCCAGCCTGCCCCCACTAAAGGACTCTGCGAGTCTGAGTGGATGGGCACCTCCGCCAGCCCATAGGGCATTGCAGACCCGGGAGTGCCCAGGCCCCGGCCGTGCTGCTCGGGCCTCCCTCGACCTGCAGTGTGGTCCCCCTTGCAG
Seq C2 exon
GTACAAGTGCGACTGTGACCCTGGGTGGAGTGGGACCAACTGTGACATCAACAACAATGAGTGTGAATCCAACCCTTGTGTCAACGGCGGCACCTGCAAAGACATGACCAGTGGCTACGTGTGCACCTGCCGGGAGGGCTTCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:13
Average complexity
IR-C
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:
PF0000822=EGF=PD(3.4=1.5),PF0000822=EGF=WD(100=58.5),PF0000822=EGF=PU(53.3=24.6)
A:
NA
C2:
PF0000822=EGF=PD(43.3=26.0),PF0000822=EGF=PU(90.3=56.0)
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:
GGAGCATGTGTAACATCAACATCG
R:
CCGGCAGGTGCACACGTA
Band lengths:
326-1298
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)