RnoINT0102219 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3915128-3916292:-
Coord C1 exon
chr3:3915721-3916292
Coord A exon
chr3:3915530-3915720
Coord C2 exon
chr3:3915128-3915529
Length
191 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTCGTCCTGTACCTCCTCAGCCC
3' ss Score
6.75
Exon sequences
Seq C1 exon
GGCTTCGAGGGTGCCACTTGTGAAAATGACGCCCGCACTTGTGGCAGTTTGCGCTGCCTCAACGGTGGTACGTGCATCTCAGGCCCACGCAGTCCCACCTGCCTATGCCTGGGCTCCTTCACTGGCCCTGAATGCCAGTTCCCAGCCAGCAGCCCCTGTGTGGGTAGCAACCCCTGCTACAATCAGGGCACCTGTGAGCCCACATCCGAGAGCCCTTTCTACCGCTGTCTATGCCCTGCCAAATTCAACGGGCTGCTGTGCCACATCCTGGACTACAGCTTCACAGGTGGCGCCGGGCGCGACATTCCCCCGCCACAGATTGAGGAGGCCTGCGAACTGCCTGAGTGCCAGGAGGATGCAGGCAATAAGGTCTGCAACCTTCAGTGTAATAATCACGCGTGTGGCTGGGACGGCGGCGACTGCTCCCTCAACTTCAATGACCCTTGGAAGAACTGCACTCAGTCCCTGCAGTGCTGGAAGTATTTTAGTGACGGCCACTGTGACAGCCAGTGCAACTCAGCTGGCTGCCTTTTTGATGGCTTCGACTGCCAGCTCACCGAGGGACAGTGCAA
Seq A exon
GTAAGTAAGGCTGGGTCGCTTCAGAGGCCCAGGGCCCAGGAGGCACCAAACCAAATACCAGGAACATGAAGCCACTGTCCGTCCCTTCCCCTAGGGGGGTCACCGAGCACATTTCCCAGGTCTGGCCCAGTTAGGGTGGGTTTGAGGCCCGCAGGCTGGGATGGGACTGACCTCGTCCTGTACCTCCTCAG
Seq C2 exon
CCCCCTGTATGACCAGTACTGCAAGGACCACTTCAGTGATGGCCACTGCGACCAGGGCTGCAACAGTGCCGAGTGTGAGTGGGATGGACTGGACTGTGCAGAGCATGTCCCCGAGCGACTGGCAGCCGGCACACTGGTGCTGGTGGTGCTGCTTCCGCCCGATCAGCTACGCAACAACTCCTTCCACTTCCTGCGGGAGCTCAGCCACGTGCTGCACACCAACGTGGTCTTCAAGCGTGACGCGCAGGGCCAGCAGATGATCTTCCCCTACTATGGCCGCGAGGAAGAGCTACGCAAGCACCCGATCAAGCGTTCTGCAGTGGGCTGGGCCACAACGTCACTGCTTCCTGGCACCAATGGTGGGCGCCAGCGCAGGGAGCTGGACCCCATGGACATCCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:25
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=0.030
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(14.7=2.6),PF0000822=EGF=WD(100=15.7),PF0000822=EGF=WD(100=16.8),PF0006612=Notch=WD(100=19.4),PF0006612=Notch=WD(100=19.9),PF0006612=Notch=PU(12.8=2.6)
A:
NA
C2:
PF0006612=Notch=PD(84.6=24.4),PF068168=NOD=WD(100=42.2),PF076847=NODP=PU(4.8=2.2)
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:
GCTGCCTTTTTGATGGCTTCG
R:
CGCAGGAAGTGGAAGGAGTTG
Band lengths:
244-435
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]