HsaINT0114823 @ hg38
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr9:136505310-136506639:-
Coord C1 exon
chr9:136506527-136506639
Coord A exon
chr9:136505882-136506526
Coord C2 exon
chr9:136505310-136505881
Length
645 bp
Sequences
Splice sites
5' ss Seq
GCGGTAGGT
5' ss Score
9
3' ss Seq
CTGTCTTCCCTCTCGGGCAGGGC
3' ss Score
9.95
Exon sequences
Seq C1 exon
GGCGCCGCTGCGAGTCCGTCATCAATGGCTGCAAAGGCAAGCCCTGCAAGAATGGGGGCACCTGCGCCGTGGCCTCCAACACCGCCCGCGGGTTCATCTGCAAGTGCCCTGCG
Seq A exon
GTAGGTGCAGGGGTGCAGGGAGGCAGGGGCCCGCCAGGGGAGACACCTGGAGAGGTCCACGTGGGGGCCTCGGGGCGCAGACCGGGCAGTGATCCTCCCGGCCTTCATCCTCCTCCTCACCCTGATGTCTTTTTTTTTTTTTTAGTTTCAATAAATGATTTTAGAGACATTTTAGATTTATAGAAAAATGGAGCAGGAAGTAGACTCCCTGGGGTGGCTGTCCCCTGCACGCAGTTCCCCTGGTTAGCAGCTTGCATCAATTTCACTCTGGATTTCAGTGATACATTGTTACCAACAGCAGCCCTTCCTGTACCTGGGGCTTGCCCTTGGCTTTGTGGTTGTGGGTTTGGGCTGAGGTATGACATGCCTGCCCACCCTCGCAGGATCACGGCAGAGAGTCCCTGCCCTAAAGTCCTCAGCACTCCACCAGTTTACCCCTTCCTCCATCTCCCGACCCCCTGGCACCCCCGATCTTTCTCTGTTGGTAGAATGTGTGTAAAGGGTTTTGCTGCTGGGGGCAAGGTTGCAGGCCGCCTCCCAGGTTAGAGGAGAGCGGTGGCACTGCTGGCCGAGGGCTGGGTGTGAGGTGGCGGGGGGGCGGGGGGTGGCCCACCCCGACACCGTCCTGTCTTCCCTCTCGGGCAG
Seq C2 exon
GGCTTCGAGGGCGCCACGTGTGAGAATGACGCTCGTACCTGCGGCAGCCTGCGCTGCCTCAACGGCGGCACATGCATCTCCGGCCCGCGCAGCCCCACCTGCCTGTGCCTGGGCCCCTTCACGGGCCCCGAATGCCAGTTCCCGGCCAGCAGCCCCTGCCTGGGCGGCAACCCCTGCTACAACCAGGGGACCTGTGAGCCCACATCCGAGAGCCCCTTCTACCGTTGCCTGTGCCCCGCCAAATTCAACGGGCTCTTGTGCCACATCCTGGACTACAGCTTCGGGGGTGGGGCCGGGCGCGACATCCCCCCGCCGCTGATCGAGGAGGCGTGCGAGCTGCCCGAGTGCCAGGAGGACGCGGGCAACAAGGTCTGCAGCCTGCAGTGCAACAACCACGCGTGCGGCTGGGACGGCGGTGACTGCTCCCTCAACTTCAATGACCCCTGGAAGAACTGCACGCAGTCTCTGCAGTGCTGGAAGTACTTCAGTGACGGCCACTGTGACAGCCAGTGCAACTCAGCCGGCTGCCTCTTCGACGGCTTTGACTGCCAGCGTGCGGAAGGCCAGTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400:ENST00000277541:24
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:
PF0000822=EGF=PD(6.1=5.3),PF0000822=EGF=PU(79.4=71.1)
A:
NA
C2:
PF0000822=EGF=PD(14.7=2.6),PF0000822=EGF=WD(100=15.7),PF0000822=EGF=WD(100=17.8),PF0006612=Notch=WD(100=19.4),PF0006612=Notch=WD(100=19.9),PF0006612=Notch=PU(15.0=3.1)
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:
TCCGTCATCAATGGCTGCAAA
R:
CAAGAGCCCGTTGAATTTGGC
Band lengths:
357-1002
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