HsaINT0114860 @ hg19
Intron Retention
Gene
ENSG00000134250 | NOTCH2
Description
notch 2 [Source:HGNC Symbol;Acc:7882]
Coordinates
chr1:120464336-120465069:-
Coord C1 exon
chr1:120464859-120465069
Coord A exon
chr1:120464433-120464858
Coord C2 exon
chr1:120464336-120464432
Length
426 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGA
5' ss Score
6.42
3' ss Seq
TCTTTTTATAATCATATTAGAAA
3' ss Score
4.79
Exon sequences
Seq C1 exon
GTGAATCCCTGACTCCAGAACGCACTCAGCTCCTCTATCTCCTTGCTGTTGCTGTTGTCATCATTCTGTTTATTATTCTGCTGGGGGTAATCATGGCAAAACGAAAGCGTAAGCATGGCTCTCTCTGGCTGCCTGAAGGTTTCACTCTTCGCCGAGATGCAAGCAATCACAAGCGTCGTGAGCCAGTGGGACAGGATGCTGTGGGGCTGAA
Seq A exon
GTAAGAGGCATTGCCAATAAGCCACTATTCACAGTATAAGTAGGGATGACTAGAAAAGCATATCTTGTTGAATCATGATTTTAAATTCTAAGCTCTGGGCATTTACTCACATTGACCATGATTCTAAATGCCTTGTGAGTGACTGAAACCACAGTCAGAGCGTGGGTGCATCTATTCTGTGTATATTATCACAATGCCGCCCAGCTTCTGTGTTGAGGTGCCCTTTTGTTGTAAGCTCACGATCAATGGGAAGGGAAAGGATGAATGCCAAGGGAATGTCACCAAAAATACTGCCCATCTTCTCTGGGCCAAGACCCTGCAAAATTGTAATATAGCCACGGGAGTGTGTCATGGTGGAAAGTGTTGAAAACCACTGTATTAGTTTATGACTGCCATTCTTATTTTTTCTTTTTATAATCATATTAG
Seq C2 exon
AAATCTCTCAGTGCAAGTCTCAGAAGCTAACCTAATTGGTACTGGAACAAGTGAACACTGGGTCGATGATGAAGGGCCCCAGCCAAAGAAAGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134250-NOTCH2:NM_024408:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.169 A=NA C2=0.545
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(14.8=12.7)
A:
NA
C2:
NO
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:
GAATCCCTGACTCCAGAACGC
R:
TTTACTTTCTTTGGCTGGGGC
Band lengths:
305-731
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)