RnoINT0102226 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3909955-3911617:-
Coord C1 exon
chr3:3911322-3911617
Coord A exon
chr3:3910103-3911321
Coord C2 exon
chr3:3909955-3910102
Length
1219 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATC
5' ss Score
4.28
3' ss Seq
AATCCATCCCTGTTTTCCAGATC
3' ss Score
9.1
Exon sequences
Seq C1 exon
ATGGCTTCACTCCCCTAATGATTGCCTCCTGCAGCGGAGGGGGCCTGGAGACAGGCAACAGTGAGGAAGAAGAAGATGCACCTGCTGTCATCTCCGACTTCATCTATCAGGGTGCCAGCTTGCACAACCAGACGGACCGCACAGGGGAGACTGCCCTGCACCTGGCTGCCCGATACTCTCGTTCAGATGCTGCCAAGCGCTTGCTGGAGGCCAGCGCAGATGCCAACATCCAAGACAACATGGGGCGTACCCCATTACATGCCGCTGTTTCTGCAGACGCTCAGGGTGTCTTCCAG
Seq A exon
GTGATCTTCCAGGTGTCTTCCAGGTGATCTTCACGCCAGTGACTGGTGTGGACCCTGCCATCTCTGATTTCAAGTGTGACTGGGCAGGGTTAACTGGCACCTCTACACGGGAACTGCACTTTGAAGGAAGTCCAGGTTACAAAGGGCACCGAGCCCCACCTGTGTTCTCTGAACAGGCTGGCTGAAGGTGGTCTTGAGGAACCTACGGGGTGAGGCAGGGCCTCCCTACCCTCAGTAAGACCCTCCAGTCTCAAGGCTGTGGCCTCGACTTGAGGTCTCCACCCCAGAGCTATAACCTTTGCAGCCTAGTCCCACCCCATTCAGCTGTGGCTGCAGGCATAGCCCATGGCAGCAGAAAGAGCTTTAGAGGCTGCTGGTTCTGGCCTGCAAACCTATCTCTTGGCTTTGCCTAGAAGCCTGGAGGCAGCCAGGGTGATTTAAGGATTTAGCTGCCTGGGTCTCCAGGGACCATCCCTAGTAGTTGCTCTTGCGTCTCGCCATCCAGTGACCCCCACTACCAAACCTGTCCTCTAGGCGGCCCTGGAGCAGGCTCCAATGGGGAACAGACCAGGCATCAAAAATCATTTAATCATTGTTGTTTAATCATTTCTTAACTTGAGCCACACTTTGTTGATCTACAGAAGAAATTAAACAAGACAGGGCAATGTACACCTGTTATCCCAGCACTCTAGAATCTGAGAGAATTGTGAGCATGAGGCTGGCCTGGTCTTCATAGAAAGACCCTGGTTCAAAATAGCAAAGAGAGGTTGAGATCAGCCCAGGGTTAAGTTGAGCTCATGGCAGGGGCTGCCTGGTGTACAGCTCTCCACACGGTCTGCTTTGCTTGCATATGCAGATGTGTGCACTTTTCTAGGCCTCTAGGCAGTGCCGAGAATCCTTACCCAGGTCACAAGTATGGCTGTGGGTCGTGAGCGGGATTCCATCCTGGCTACCCTGCCCTCTGTCCCCCATGCTATTCAGTTTGATTTCTTTAGCCTGGAAGTAATTCTGACAGCCATGACCAAAAAATGAGGCCACCTGTGGTCCCAGTGGGTCCCCAACACAGCCCCTCCTGTACATGAAATACAGCTCCATAGCATCCAGTCTTCCTCAGGGGCTCATCCGAGTCACGGGAGCAGCTGAGCCCCGTCCAGGCATTGGTTCCTGGAGGTATGGGCTTGTGTTTAGCTCACTGCCTGAATCCATCCCTGTTTTCCAG
Seq C2 exon
ATCCTGCTCCGGAACAGAGCCACAGATCTGGATGCCCGAATGCATGATGGCACAACCCCTCTGATCCTGGCGGCACGCCTGGCCGTGGAAGGCATGCTAGAGGACCTCATCAACTCTCACGCTGATGTCAATGCTGTGGATGACCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.424 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(79.7=100)
A:
NA
C2:
PF127962=Ank_2=PD(10.6=26.0),PF0002325=Ank=WD(100=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGCACCTGCTGTCATCTCC
R:
GCGTGAGAGTTGATGAGGTCC
Band lengths:
344-1563
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]