RnoINT0102208 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3921553-3923630:-
Coord C1 exon
chr3:3923517-3923630
Coord A exon
chr3:3921673-3923516
Coord C2 exon
chr3:3921553-3921672
Length
1844 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
CTACGTATCTTTCTTTCTAGGAG
3' ss Score
10.13
Exon sequences
Seq C1 exon
GCCCTAACTGCCAGACCAACATTAACGAATGTGCTTCCAACCCCTGCCTGAACCAGGGCACCTGCATTGATGATGTCGCTGGGTACAAATGCAACTGCCCTCTGCCCTATACAG
Seq A exon
GTATGAGCAGCCAGGGACTGTAATTGGCTCTGGTGGTAGCTAGTGGGGCCGAGAGTGTATGGGCTCACCAGGCATTGGAGAAGGTTCTGCTCCTCACTGAGTGGGGATCTTGGATCCTGCGGCACTTGGGCCTGGGGATTAGTCCCCAGATGAGCAAATACAGAGGGTGCCTAGGAGGAAGCTCCAGGGTGTGTGTATCCAGGTGTTCACCTGGCATGTCTGGAGTGAGGGGAGCCCTGGACTCCTCCAGAGAAAGTCCAGGGGCCTGACTGGTAGAGACTGAATGGATCACGGTCCACTTTGCCTGTGCCTCTGGGGGCCCTGGCTGCCCTCCTCCTCTGGCTGAGCCTGGGATTCCTTTGATGGCAGCTTCTTTGTGTGAGGAGACAAGGAGCCCTCTGTTCAGATGAACAGTGGCAGCTCCTGCCATGGGCACTGCCTGAGGAATGGCGAGAAGTAGACCCCCTGCAGGAGAGATGTGCATTGAACATGAAAGCCATGGCCACATTGCCCCCCAACCCCTGCAGCTCCCAATACTGCCACTGAATACTGGTGGCTTTCTTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTACTGGGTTCTGGACATCGCAAGTGGGTCTGTGAAGGTGGAGCCCTTCCAGTTCCTATGGTGCTTTGCAGCTAGTGACCAGGATGCTGTTTTCTTTGACAAAGTTAAAGGGCCTGGATTTTGTCTCCTGCGTTGGTCAGTGAGGAAACTGTCAGCCGCCAGGCACACCCCTTGTCCCTTTTGGTCCTGTTGCTATCGAGGCTGGCGGGAGGAGTCAAGCCGCGCTGACCAGCTTCCTGCTGGCCTGCTTCCTGCTTCCCTTTGCACAATTGTCGGAAACTCTGTCAAAGTTCCTGTCTGCCCAGGTCACCGTGGAAACCGATAGAGAGAGAGGCCCTGGAGACTCTCACCAGCGGGCTGGGGACATGGTGGGAGACAAGGAAGATAAGGCTTCCTTGCTTAGCTCCTGGAGCCAACCATGGCCATAAACAGGAAAGCTAGCTGGGATTATGAGGAGTCACCTGGGTCACGCATGGCTCCCCCAGGCGGTTATCAGATGCACTGCCCTAGTGTGAGGCTGCACCCCGTGTAGGATGTGCTTGGGGTAGCCATGGTAGCTCTGTCTCAGGAGTGACCTAAAACCTCAGGATCAGCTCAAGGTTTTTCCTGGAATGGGCACCAGGCCAGGGTCCTCCAGGCTCAACCACCTGTTATAGTAGGGTTTTGTTTTGAGGTTCTCTGGTTGAGCAAGGCCCAGGTTTTATCTCGCAGCATTTGGAAGATGAGCAATGGCTTCTGGGATTAGATAGATGGCTCCTGGAGAAAGAGTGCTTATTGTGGAAACCTGAGACCTGTTCCATGAAAACTGGGTACCGTAACCCCAACATTTGGGAGCACAGACAGATGTATCTTGAGAGCTCACTGACTGGCCATCCTAGCTAAAATGATGGCAGGCTTCTGATTCAGGGAGACTGTCTCAAAGGAATAAGGTGCAGGGTTGGTCGAGGACCCCTGACCTCCATCTCTGCTTCTGCATACACACTTGTGTGTACTTACATGCCCATGTGCATACACTATACACTTTTTAAAAAAGTAGCTTCAGAGAGAAACTTGATTCTGCTTTATCTCTAACTTCCTGTCTGCAATCGTCATTCCTCCCGGGATCAGAGTCTGGCTGGCCAATCATACAGCATCTCCTATACTCCCCCAGCCCCTCTATGGAAGACACTGTGGGCCAGGTTAGCTGGGTCCTATCTACTACGTATCTTTCTTTCTAG
Seq C2 exon
GAGCCACATGTGAGGTGGTGTTGGCCCCATGTGCCACCAGCCCCTGCAAAAACAGTGGGGTATGCAAGGAGTCTGAGGACTATGAGAGCTTTTCCTGTGTCTGTCCCACAGGCTGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:15
Average complexity
IR
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(6.5=5.1),PF0000822=EGF=PU(90.3=71.8)
A:
NA
C2:
PF0000822=EGF=PD(6.5=4.9),PF0000822=EGF=PU(90.9=73.2)
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:
GCCCTAACTGCCAGACCAAC
R:
TGGGACAGACACAGGAAAAGC
Band lengths:
222-2066
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]