HsaINT0114839 @ hg38
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr9:136515981-136517385:-
Coord C1 exon
chr9:136517272-136517385
Coord A exon
chr9:136516095-136517271
Coord C2 exon
chr9:136515981-136516094
Length
1177 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
CCTCCCCTCCCCGGCCCCAGGCT
3' ss Score
8.44
Exon sequences
Seq C1 exon
GCTACGAGGGTGTGCACTGCGAGGTCAACACAGACGAGTGTGCCAGCAGCCCCTGCCTGCACAATGGCCGCTGCCTGGACAAGATCAATGAGTTCCAGTGCGAGTGCCCCACGG
Seq A exon
GTGAGGGCCACCCCCGCCCCCTGCCCCCGGGTCGTCTGCACCCTGGCCTCCTGAGGGGTGCCTGGGCGTGGGTTGTGTCCCCTGCCCCCGGGCCATCTGCACCCCGGCCTCCTGAGGGGTGAGGGCCGCCCCCACCCCCTGCCCTCGGGCCGTCCGCACCCCGGCCTCCTGAGGGGTGAGGGCCGTGGGTTGTGTCCCCTGCTCCTGGGCCGTCTGCACCCCGGCCTCCTGAGGGGGGCCTGGCCGTGGATTGTGTCCCCTGCCCCTGGGCCGTCTGCACCCCGGCCTCCTGAGGGGTGCCTGGCCGTAGGTTGTGTCCCCTGCCCCTGGGCCGTCTGCACCCCGGCCTTCTGAGGGGGGCCTGGCCATTGGTTGTGTTCAGATTCCCAGGAGAGCGAGGGTTTTGCCTCATGAGTGGATGGGAGTGTTTTCAGACTTCCCCGAAGGAAGGGCAGGGCCCAGTGGGGAGTGGGAGCTTGCCCAGGGGTCGCGGTGGAGCCCAGGGCCAGGAGATCCTCCTTGATCTGGGTGCAGCCCCTTCTGCCTGGAGAGAAGGGTATACCAGGAGCTGCAGTGCCCAGACAGGGAGGAGGCTCCAGCCTGGCTTTCTGAGGGCTCGATGCTGGGAGGGAGGCCAGCCTGCCCTGTCCTGCCATGTCCCCTGCCCAACGGCACGCCAGCGACAAGGGTATGCAGAGAACCACGTGGGGCAGGTTGGCCTGCAATGGAGATGATGGCTGCCCGGGGCGGACTTGGAGGAACTCTCAGGGGCCTGGGTGAAAGGTGTTTCCATCTGTCCCAGAGCTGGGGGCCGGGGCGCAGAGCCCAGGGAGGCGTTGCCAGCCCAAGCCTAGGCTCCCAAGACATAGATTACCCGTCCCAGACACTGGAGCGAGGGGAGCCCCATTCTCAGCCCGGCTCCACTGTAGCCATAGCAACCCAGTCGGTTTGGGAAAAAGGCCCCTTCTGTGGGAGCGAGGGCGTGTGGTGCTGGGGGAGGGGCTTTGATCCGGGGAGCGGGCAGCGGGAGGCAGGGAGAGCTGGAGCTGGCTGAGCTCAGGCTGAGTGTGCCCTGGGGAGCCCAGCCAGGCGCTCACTGCTGGGGTCTGGCCAGGGGTCCCTGAAGGGCCATAGTGCTGTTGCACATGACTCCCTCCCCTCCCCTCCCCGGCCCCAG
Seq C2 exon
GCTTCACTGGGCATCTGTGCCAGTACGATGTGGACGAGTGTGCCAGCACCCCCTGCAAGAATGGTGCCAAGTGCCTGGACGGACCCAACACTTACACCTGTGTGTGCACGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400:ENST00000277541:9
Average complexity
IR
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:
PF0764510=EGF_CA=PD(25.0=25.6),PF0000822=EGF=PU(80.6=64.1)
A:
NA
C2:
PF0000822=EGF=PD(16.1=12.8),PF0000822=EGF=PU(80.6=64.1)
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:
GCTACGAGGGTGTGCACTG
R:
CAGGTGTAAGTGTTGGGTCCG
Band lengths:
214-1391
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