HsaINT0114833 @ hg19
Intron Retention
Gene
ENSG00000148400 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:7881]
Coordinates
chr9:139388896-139393448:-
Coord C1 exon
chr9:139393351-139393448
Coord A exon
chr9:139392011-139393350
Coord C2 exon
chr9:139388896-139392010
Length
1340 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
CCCCCGCCCTCATCCCCCAGGAG
3' ss Score
11.86
Exon sequences
Seq C1 exon
GCAAGTCCGCCCTGCACTGGGCCGCCGCCGTGAACAATGTGGATGCCGCAGTTGTGCTCCTGAAGAACGGGGCTAACAAAGATATGCAGAACAACAGG
Seq A exon
GTGAGCGCGAGGCTGGGATGCCAGGGGAGACGTGAGGGCTGAATCCACAGAGAAGTGAGGGCCAAACCCACGGGGCGCAGGGACACAAGGGCCTGACCCACAGGGTCTCGAGGGTCGCTGGGCCCGCATGTGGGCCCCACCCGCATGATGCGGGCACCTCGTTAGTGCTCCTGCCTTCCTTCAGCCCCCGTTTATGGAGCCCTTCCAAGTGCAGGTCCAGCTGTCAGGACACGGCGGCTCGCCCCTCAGACCCAGCCCTACCCTCCTGGGCGGCAGTCATGGCGGGGCACACAGCCTGGCGTGGGGAACGCTGCTGCTGCCACTGCTGTGTCACCGTCACCTGGACCTCACCTTCTGTCCCCAGCTGTCACCAGGCGGGGGTGGGGATGGGAATGTGGTGACGCAGGTGGTGCAGATTGAGCCAGAACACGCGTGGCGGCAGCTCCCTGCGGGGCGGGGCCTCTTGGTGTGTTCACCAAGGCCAAGGACCTCAAGGCTCAGAGGAAGAAGTCTCAGGACTATATCCAAGGGGAGCCACCCCCAGCCCTCATCCTGGCCCTGCAGCTCCTGGCCCTGCAGCTGCTGTTGGTTTCCCCTGGGTGCTCAGGGCACAGGTGCAGACACCCCCACCTCCCTGCCGCCAGAACCCCCACCCCCGCCCCCAACTCCTGCTGCCCCCTTGGCATGTCAGGCTCAGGCGTCTCTCCCTCCTGGGTGAGGGCACACAGCGGGCCTGGGCACCGGGGCATGTTGGCCCAGGCGCTCCCCAGTCCGTGGCAGCATGGCCCCACAGAGACTGGGCCCCAGAGGGCATCAAGGCCTGGGAAGCCCCTTCCCACTCCCACACAGCAGCCTCACCCAGACCTGTGACGTGTCCACCGCACAGAGGAGACCCCAGGAAGGAGCTTGGTGGCCACCAGGGTGGCTTGATGGCCGTCCAGATGACGAGCTCCCTCCCTGGTGCCCTCGCCGGTGCCTCTGAACCGCTCCAGGAATTTCCTTTTGTGCCTTATTGGGGGCAGGGAAGAGGGCCTGCAGTTGGTTAGATTTTCAGTGGGGTCTGTGACCCCCCCATAGAGGTGGAGCCCCGCTGATCTAGGGTAGAGGACTGCACAGATCCCCTCTCTGGGTGGGTTTCAGAAGATGTATCAAAGCCTTAACATTTAACAAGAGTCAGGCTAGGTGGTTGCAGGACGCTGGGGTGGGGTCCTGAGGAGCAGCCTGCCTGCCCCCACCCCGCGGAGGAGGTTGTACTGCTGCTTCCTCTGGTGATGGAACCTTGGGGAGGGTCCCCACGCCTGGCCTGGCCCCCCTCACCGGCCCCCGCCCTCATCCCCCAG
Seq C2 exon
GAGGAGACACCCCTGTTTCTGGCCGCCCGGGAGGGCAGCTACGAGACCGCCAAGGTGCTGCTGGACCACTTTGCCAACCGGGACATCACGGATCATATGGACCGCCTGCCGCGCGACATCGCACAGGAGCGCATGCATCACGACATCGTGAGGCTGCTGGACGAGTACAACCTGGTGCGCAGCCCGCAGCTGCACGGAGCCCCGCTGGGGGGCACGCCCACCCTGTCGCCCCCGCTCTGCTCGCCCAACGGCTACCTGGGCAGCCTCAAGCCCGGCGTGCAGGGCAAGAAGGTCCGCAAGCCCAGCAGCAAAGGCCTGGCCTGTGGAAGCAAGGAGGCCAAGGACCTCAAGGCACGGAGGAAGAAGTCCCAGGACGGCAAGGGCTGCCTGCTGGACAGCTCCGGCATGCTCTCGCCCGTGGACTCCCTGGAGTCACCCCATGGCTACCTGTCAGACGTGGCCTCGCCGCCACTGCTGCCCTCCCCGTTCCAGCAGTCTCCGTCCGTGCCCCTCAACCACCTGCCTGGGATGCCCGACACCCACCTGGGCATCGGGCACCTGAACGTGGCGGCCAAGCCCGAGATGGCGGCGCTGGGTGGGGGCGGCCGGCTGGCCTTTGAGACTGGCCCACCTCGTCTCTCCCACCTGCCTGTGGCCTCTGGCACCAGCACCGTCCTGGGCTCCAGCAGCGGAGGGGCCCTGAATTTCACTGTGGGCGGGTCCACCAGTTTGAATGGTCAATGCGAGTGGCTGTCCCGGCTGCAGAGCGGCATGGTGCCGAACCAATACAACCCTCTGCGGGGGAGTGTGGCACCAGGCCCCCTGAGCACACAGGCCCCCTCCCTGCAGCATGGCATGGTAGGCCCGCTGCACAGTAGCCTTGCTGCCAGCGCCCTGTCCCAGATGATGAGCTACCAGGGCCTGCCCAGCACCCGGCTGGCCACCCAGCCTCACCTGGTGCAGACCCAGCAGGTGCAGCCACAAAACTTACAGATGCAGCAGCAGAACCTGCAGCCAGCAAACATCCAGCAGCAGCAAAGCCTGCAGCCGCCACCACCACCACCACAGCCGCACCTTGGCGTGAGCTCAGCAGCCAGCGGCCACCTGGGCCGGAGCTTCCTGAGTGGAGAGCCGAGCCAGGCAGACGTGCAGCCACTGGGCCCCAGCAGCCTGGCGGTGCACACTATTCTGCCCCAGGAGAGCCCCGCCCTGCCCACGTCGCTGCCATCCTCGCTGGTCCCACCCGTGACCGCAGCCCAGTTCCTGACGCCCCCCTCGCAGCACAGCTACTCCTCGCCTGTGGACAACACCCCCAGCCACCAGCTACAGGTGCCTGAGCACCCCTTCCTCACCCCGTCCCCTGAGTCCCCTGACCAGTGGTCCAGCTCGTCCCCGCATTCCAACGTCTCCGACTGGTCCGAGGGCGTCTCCAGCCCTCCCACCAGCATGCAGTCCCAGATCGCCCGCATTCCGGAGGCCTTCAAGTAAACGGCGCGCCCCACGAGACCCCGGCTTCCTTTCCCAAGCCTTCGGGCGTCTGTGTGCGCTCTGTGGATGCCAGGGCCGACCAGAGGAGCCTTTTTAAAACACATGTTTTTATACAAAATAAGAACGAGGATTTTAATTTTTTTTAGTATTTATTTATGTACTTTTATTTTACACAGAAACACTGCCTTTTTATTTATATGTACTGTTTTATCTGGCCCCAGGTAGAAACTTTTATCTATTCTGAGAAAACAAGCAAGTTCTGAGAGCCAGGGTTTTCCTACGTAGGATGAAAAGATTCTTCTGTGTTTATAAAATATAAACAAAGATTCATGATTTATAAATGCCATTTATTTATTGATTCCTTTTTTCAAAATCCAAAAAGAAATGATGTTGGAGAAGGGAAGTTGAACGAGCATAGTCCAAAAAGCTCCTGGGGCGTCCAGGCCGCGCCCTTTCCCCGACGCCCACCCAACCCCAAGCCAGCCCGGCCGCTCCACCAGCATCACCTGCCTGTTAGGAGAAGCTGCATCCAGAGGCAAACGGAGGCAAAGCTGGCTCACCTTCCGCACGCGGATTAATTTGCATCTGAAATAGGAAACAAGTGAAAGCATATGGGTTAGATGTTGCCATGTGTTTTAGATGGTTTCTTGCAAGCATGCTTGTGAAAATGTGTTCTCGGAGTGTGTATGCCAAGAGTGCACCCATGGTACCAATCATGAATCTTTGTTTCAGGTTCAGTATTATGTAGTTGTTCGTTGGTTATACAAGTTCTTGGTCCCTCCAGAACCACCCCGGCCCCCTGCCCGTTCTTGAAATGTAGGCATCATGCATGTCAAACATGAGATGTGTGGACTGTGGCACTTGCCTGGGTCACACACGGAGGCATCCTACCCTTTTCTGGGGAAAGACACTGCCTGGGCTGACCCCGGTGGCGGCCCCAGCACCTCAGCCTGCACAGTGTCCCCCAGGTTCCGAAGAAGATGCTCCAGCAACACAGCCTGGGCCCCAGCTCGCGGGACCCGACCCCCCGTGGGCTCCCGTGTTTTGTAGGAGACTTGCCAGAGCCGGGCACATTGAGCTGTGCAACGCCGTGGGCTGCGTCCTTTGGTCCTGTCCCCGCAGCCCTGGCAGGGGGCATGCGGTCGGGCAGGGGCTGGAGGGAGGCGGGGGCTGCCCTTGGGCCACCCCTCCTAGTTTGGGAGGAGCAGATTTTTGCAATACCAAGTATAGCCTATGGCAGAAAAAATGTCTGTAAATATGTTTTTAAAGGTGGATTTTGTTTAAAAAATCTTAATGAATGAGTCTGTTGTGTGTCATGCCAGTGAGGGACGTCAGACTTGGCTCAGCTCGGGGAGCCTTAGCCGCCCATGCACTGGGGACGCTCCGCTGCCGTGCCGCCTGCACTCCTCAGGGCAGCCTCCCCCGGCTCTACGGGGGCCGCGTGGTGCCATCCCCAGGGGGCATGACCAGATGCGTCCCAAGATGTTGATTTTTACTGTGTTTTATAAAATAGAGTGTAGTTTACAGAAAAAGACTTTAAAAGTGATCTACATGAGGAACTGTAGATGATGTATTTTTTTCATCTTTTTTGTTAACTGATTTGCAATAAAAATGATACTGATGGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148400-NOTCH1:NM_017617:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.212 A=NA C2=0.786
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(34.4=100)
A:
NA
C2:
PF127962=Ank_2=PD(32.3=6.0),PF119363=DUF3454=WD(100=12.9)
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:
TCCTGAAGAACGGGGCTAACA
R:
GGGCTTGCGGACCTTCTTG
Band lengths:
344-1684
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)