RnoINT0102225 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3911322-3912584:-
Coord C1 exon
chr3:3912419-3912584
Coord A exon
chr3:3911618-3912418
Coord C2 exon
chr3:3911322-3911617
Length
801 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CATTTCTGTCCTCTCTGCAGATG
3' ss Score
12.24
Exon sequences
Seq C1 exon
TTTGAGGAACCAGTGGTTCTCCCTGACCTGGATGATCAGACTGACCACCGGCAGTGGACCCAGCAGCACCTGGATGCCGCTGACCTACGTGTGTCTGCCATGGCCCCAACGCCGCCTCAGGGGGAGGTAGATGCTGACTGCATGGACGTCAATGTTCGAGGACCAG
Seq A exon
GTAAGGCCACTGGAGATGCATGCACACAGCCCCTAGCATAGACTTAGAGGCCGGTAGGGATTGAGGAGGACTGGGGCACCGAGCGGCTCTGCCGCCACCCCCAGAATACACTTTTTCATGAAATGCTGCCTTTTGTTAGTCAAAGTGTTAATGTTTGTTTGTTTGAGACAGGGTCTTACTCTGTAGACCAGGCTAGCACCAAATATGATTTTTTTGTCTCAGCTTCTAATATGCTGGAATTATAGGTGTGGTCCCATGCCCAGCTAAAGTGTTGACTTTTAAAATTATATGCATATATAGGTGTATATAAAATATATACATATACATTTTATTTTATGTGCGAGGTCCTGCCTACATATGTGTGTGTGTGTGTCATGTGCATGCCCAGTGCCTGTGGGAAGCCTGAAGAAGCCAGTGGATCCCCTGGAACTGGAGTTACCGATGGTTGTGAGTGGCCCTGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGCACTGGCTATCTCTCTAACCCTTATTTTATGTTTTAAATCATGTATTCATTTGAGTACAAGGGGCACACATGTACCGTGGTGCACACGCGGAGGTCAGAGGACAACTTGCCAGGGCAGGTTCTCTCCTGCCATGTTGGTCTCAGGGTATCTTCCAGGTGGGCACCACTGCGTCCTTGGGGACCTCGTCTGGGGTCCCTTAAACTGAAGGCCGTGTGGAAGGACCGCCAGGGCCAGGGTTGGATGTTGGCCCTCCCTGAGGCGGACATCACCCTTCCCACACCTACCCATTTCTGTCCTCTCTGCAG
Seq C2 exon
ATGGCTTCACTCCCCTAATGATTGCCTCCTGCAGCGGAGGGGGCCTGGAGACAGGCAACAGTGAGGAAGAAGAAGATGCACCTGCTGTCATCTCCGACTTCATCTATCAGGGTGCCAGCTTGCACAACCAGACGGACCGCACAGGGGAGACTGCCCTGCACCTGGCTGCCCGATACTCTCGTTCAGATGCTGCCAAGCGCTTGCTGGAGGCCAGCGCAGATGCCAACATCCAAGACAACATGGGGCGTACCCCATTACATGCCGCTGTTTCTGCAGACGCTCAGGGTGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.804 A=NA C2=0.424
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(8.1=17.9)
A:
NA
C2:
PF127962=Ank_2=FE(79.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCTACGTGTGTCTGCCATG
R:
CAGCGGCATGTAATGGGGTAC
Band lengths:
352-1153
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]