HsaINT0114825 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139397634-139399556:-
Coord C1 exon
chr9:139399125-139399556
Coord A exon
chr9:139397783-139399124
Coord C2 exon
chr9:139397634-139397782
Length
1342 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTCTCTGATTGTCCGCCCAGCTC
3' ss Score
5.87
Exon sequences
Seq C1 exon
CCCCCTGTACGACCAGTACTGCAAGGACCACTTCAGCGACGGGCACTGCGACCAGGGCTGCAACAGCGCGGAGTGCGAGTGGGACGGGCTGGACTGTGCGGAGCATGTACCCGAGAGGCTGGCGGCCGGCACGCTGGTGGTGGTGGTGCTGATGCCGCCGGAGCAGCTGCGCAACAGCTCCTTCCACTTCCTGCGGGAGCTCAGCCGCGTGCTGCACACCAACGTGGTCTTCAAGCGTGACGCACACGGCCAGCAGATGATCTTCCCCTACTACGGCCGCGAGGAGGAGCTGCGCAAGCACCCCATCAAGCGTGCCGCCGAGGGCTGGGCCGCACCTGACGCCCTGCTGGGCCAGGTGAAGGCCTCGCTGCTCCCTGGTGGCAGCGAGGGTGGGCGGCGGCGGAGGGAGCTGGACCCCATGGACGTCCGCGG
Seq A exon
GTGAGTGAGACCCGGCGCCCACGGTCAATCCCCGCAACTCTCCTGGGCCCTCCCCGACGGCCTCCCTGCCCCTCACGGCCGGCGCCATGGCAAGCAGTACTCTCCCCACTTTATGGTAAAAGAGACGGAGGTTCCGAGAGGACCTGGGACTTCAGGGCCTGCGCAGGCAAGGAGTAGAGGCAGCATTCCAGCTCAGGGCCCTGACCCCACAGCCACACCCTTTTCCTGGGCCACTGCCTTCCCCTGGACAGGCGGCACTCCTGTGCCCAGTAGGTGATTTTGAGATTGAGCTGTGCCTTAGGCACTGGATACTACACTGATTAAAACTCAGCCCTCTGCCAGGCGAGGAGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGCGGAGCCCTTGAGCCCAGGAGTTCGAGACCAGTCTGGGCAACATAGGGAGACCTTGTCTCTGTTTTTTTTAAAAAAGTATTAAAAGAAGTAAAAAACAAAACACTCAGCTCTCCAGGGGTTCCCACAGGGCTGAACAGCCCCACCCCAGACAAGAATGCCGCTTGGTCATGGCGTCTGCCTGGCTTGGGCTGGAGAGGAGGCAGGTGGAGGTCCTGGGAGGGGGCATTGCTGGGCCTTGCAGTTGGAGGAGGAGCTGGTGGGGGTGGGGGGTCCCACGGTGGGAGAACACAGGCAGGAGCAGCTTGAGTGCAGGGGGCACCCCACAAGGCTCCCGCCCATGCCTACTCGATCTGGGGCAGCTGGACCCAGGAGCCAGGTTGGTTGTGCCCTTCGTGTGCCTGACCCTGGTGGGTTTGCCTGTCAGTTCTGCTGGCTTGGAGCAATCCTGGAGGTCAGAAGCATCATCTCACAGGCTGGATGGGATCCTGCTCACGGGAACCCAGTCCTGGGGAGCAGAGCTCACCCCCAGCCAGCCTCACCACACAGCCCACCACCGCTGCACCCACCCCCACCTCACGCCTGTGCTTCCTGCAGGGCCTGGGGATGGCTCCTGGGGGAGGACTGGGCTCCTGGCACATACTCTGTCCTGAGATGAGGAAACGTGTCTGTGGCACCAGCAGGAGCCAGAGAGGGTGTCAGGGCGGGCCAGGGAGAGCGCGTTGGTGGGTATCTGGGATGAGCCGTGATCAGCACTGGCCGGAGTCGGGGGGCTGGCACCAGTCCCCTGCAGGGTAGCTGCTGTCAGACCTGGCTTCCCACCACCCCAGGCTGCCTCACCATGTCCTGACTGTGGCGTCATGGGCCTCAGTGTCCTGCGGCAGCATCCCTGGCCGGTGGGCGGGGGAGGAGGAAGCCTCGGGTCCCAGCCCCTCTCTGATTGTCCGCCCAG
Seq C2 exon
CTCCATCGTCTACCTGGAGATTGACAACCGGCAGTGTGTGCAGGCCTCCTCGCAGTGCTTCCAGAGTGCCACCGACGTGGCCGCATTCCTGGGAGCGCTCGCCTCGCTGGGCAGCCTCAACATCCCCTACAAGATCGAGGCCGTGCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=0.039
Domain overlap (PFAM):
C1:
PF0006612=Notch=PD(82.5=22.8),PF068168=NOD=WD(100=39.3),PF076847=NODP=PU(4.8=2.1)
A:
NA
C2:
PF076847=NODP=FE(79.4=100)
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:
CAACGTGGTCTTCAAGCGTGA
R:
GGCCTCGATCTTGTAGGGGAT
Band lengths:
355-1697
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)