HsaINT0114844 @ hg19
Intron Retention
Gene
ENSG00000134250 | NOTCH2
Description
notch 2 [Source:HGNC Symbol;Acc:7882]
Coordinates
chr1:120496166-120497855:-
Coord C1 exon
chr1:120497663-120497855
Coord A exon
chr1:120496312-120497662
Coord C2 exon
chr1:120496166-120496311
Length
1351 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
AAAGTTTTGTCTTCTTTCAGATA
3' ss Score
9.9
Exon sequences
Seq C1 exon
GGCAGAGATGTAACATTGACATTGATGAGTGTGCCTCCAATCCCTGTCGCAAGGGTGCAACATGTATCAACGGTGTGAATGGTTTCCGCTGTATATGCCCCGAGGGACCCCATCACCCCAGCTGCTACTCACAGGTGAACGAATGCCTGAGCAATCCCTGCATCCATGGAAACTGTACTGGAGGTCTCAGTGG
Seq A exon
GTGAGTAGCTGCCCCATGTGATAGTTTCTTATTGACCTGTGTTAAGCCAGTTGGCTTGTAGTACTGGTGACAGCCTGAAGTTGTCAAATGGGGCTTTGAGCTGAAACTTTGCTGAAGATTTGGTAGTCTGCATCAAAGCCTTCTGAATTACCATTTAATCCATGGAAGCTGGCCCCTCCCTTCCATAAGTGAGGACCTAGATGGAACATAAGGAGGAATGTCTCCCTTATATGGGTCATTAGCAAGGACCTCATGGGAGGAACCCATACTCATTGTATGAATCTTTGGCAGTTATGTTTTTAGTATGTATTACTGGAATGATTTCTGAAGAATGTTCTAGCTTTTGATTTTTTTTCCCCTGCTTAAACATAGCTCAGCTCTGTTCTGTCACAGTGCCAGTGTGTGCTCTGAAGTAGGGCCGCTTCAGCCAACTTTAGAAATGTCCCTGATAAAACATTTGCAATTTTTAAGCCCCACAGACTTGTGTGATGTGTTAGTGATTTTCTAGAATCATAGAGTGACCTTAGGTCTCACGAGACGCTCTTATACTCTTGCTGCATTTGCCATAGGATATGGCTTTGGACATTTTCCTTTGCCAAACTTTGAAAGATGAAAGGATAAAGAGTGTTTAGTGGCAAATAGTAAATAAAGTTATTTAAAAATTAATTAACTCAGTATTGGTGTTTCAGAGTATAGCAGCCTTCAAGGCACCCTTATCCATCTCTCATTTTCTTAAAATTCTCCCGATAAGAAAGCTATCATTTCCTGATATCACATTCTAAGTGTTAGTGATGTTCAAATTGGAGATTATATTTACAATTCAAATACCTTCATTCCTGTGCCTTTTCCTGCAGAATACCCTAGGTGCTTTCTGAAGCCAAGTGTTAGGTCAAGACAAAGCATGACTTAGATATGAAATATCCCAGGAGCATCTTAGAGTGGCTCAGGGTCCCTGACAGTGACCTAGGTATCTATTTGGCACCAAAAACTAATGATCTTAATGTTTGCTTTACTTTAGTTTTATGTATAATAACATACATTGTGCAGATTTATCCATGATATTGTTTCCTTCAGAGTGGCCCAATATATTGTAGAAACCATTGTTTACATAAGAAATTTCATTATAATTTCACTAACTTAGTGAGCCAGGAAAGCACCAAGAAGGTTTCTTTACTGGATACACCTGATAGGGCCACATGGTACACACCATGTGCAAGGTGATGCAAGGATAGTTCCATGAAAGTAGAAATGAGATCAGTTTACCCCATTTCTTCACCAAGTCCTGTATTTCACTCTATGACTCAATCATACGTTTATACCTCCTATAGTAAAAAGTTTTGTCTTCTTTCAG
Seq C2 exon
ATATAAGTGTCTCTGTGATGCAGGCTGGGTTGGCATCAACTGTGAAGTGGACAAAAATGAATGCCTTTCGAATCCATGCCAGAATGGAGGAACTTGTGACAATCTGGTGAATGGATACAGGTGTACTTGCAAGAAGGGCTTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134250-NOTCH2:NM_024408:13
Average complexity
IR-S
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(6.7=3.1),PF0764510=EGF_CA=WD(100=55.4),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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGAGATGTAACATTGACATTGA
R:
AAGCCCTTCTTGCAAGTACACC
Band lengths:
334-1685
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)