RnoINT0102220 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3914140-3915529:-
Coord C1 exon
chr3:3915128-3915529
Coord A exon
chr3:3914289-3915127
Coord C2 exon
chr3:3914140-3914288
Length
839 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
ACTGTGCTGTGTGTTCTCAGCTC
3' ss Score
9.46
Exon sequences
Seq C1 exon
CCCCCTGTATGACCAGTACTGCAAGGACCACTTCAGTGATGGCCACTGCGACCAGGGCTGCAACAGTGCCGAGTGTGAGTGGGATGGACTGGACTGTGCAGAGCATGTCCCCGAGCGACTGGCAGCCGGCACACTGGTGCTGGTGGTGCTGCTTCCGCCCGATCAGCTACGCAACAACTCCTTCCACTTCCTGCGGGAGCTCAGCCACGTGCTGCACACCAACGTGGTCTTCAAGCGTGACGCGCAGGGCCAGCAGATGATCTTCCCCTACTATGGCCGCGAGGAAGAGCTACGCAAGCACCCGATCAAGCGTTCTGCAGTGGGCTGGGCCACAACGTCACTGCTTCCTGGCACCAATGGTGGGCGCCAGCGCAGGGAGCTGGACCCCATGGACATCCATGG
Seq A exon
GTGAGTGAGCTCCTGCCACTGTGGGCTGGTTCCCGGTGTGTCCCTGGGTTCTCGAACCAGCTCATCCCTGGAGCTGTGACCTCACCTTACCTTAAGGTCAGAAAGCACCAGGAACGATGAGGCCATCCTTCTGCTGGATGCCCAGTGTTTGCCCGTTGTGACTGTCAGGCCCCACCGTGTACCATGTGTTGGAGACCAGGCTGATGTCCCCTGGGGCTAAGCCATCCTAGGCCAATCCTGCACCTCAGTTGTAGTGACTCATCCATACCACAGAAGAGGAGTGAGGGGTACACAAGGGCGCTCTTGCTGAGCCTTAAAGGCCGAGGAGCCTAGGGTGGCGGTGAGGAGGCAGAGATAAGAGTGTCTCCTGGAGGGGTTGGGGATTTAGCTCAGTGGTAGAGCACTTGCCTAGCAAGCGCAAGGCCCTGGGTTTGGTCCCCAGCTCCGAAAAAAAGAAAAAAGAAAAAGAAAAAAAAGAAAGAGCTGGCTCTCTGGCATCTGAGCCTGCTATTGCCTCAAGCTACCCACTAGGGAGTCACAACTGCATCCCTGCACTTCTGTGGGGCACCAGGCACTGCTCTCAAGAGGGCATTGTATGCCTAGAGGCTATCTGTTCTCTGAAGTGAGGAAAAGGGGCGCTGTGCACCTAAGGGGCAAGGCTGGACAATAGAATGAGCCCCTGCCGAGTGCTAAAAAACTGGGGCTGCAGGGAGACTGTTCCACTGCAGGACTGTTGTCTGATATGCCCTCGGGGGGTCAGGGAGATAGGTAGGGAGTCAGAGCTGTGTGCCCGCAGCACACTGGAGTGTATCTGATCTCACTGTGCTGTGTGTTCTCAG
Seq C2 exon
CTCCATCGTCTACCTGGAGATCGACAACCGGCAGTGTGTACAGTCATCCTCGCAATGCTTCCAGAGCGCCACCGATGTGGCTGCCTTCCTAGGTGCTCTTGCCTCCCTCGGCAGCCTCAATATCCCCTACAAGATCGAAGCCGTAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.030 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006612=Notch=PD(84.6=24.4),PF068168=NOD=WD(100=42.2),PF076847=NODP=PU(4.8=2.2)
A:
NA
C2:
PF076847=NODP=FE(79.4=100)
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:
TGAGTGGGATGGACTGGACTG
R:
CCGGTTGTCGATCTCCAGGTA
Band lengths:
358-1197
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]