RnoINT0102224 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3931623-3932799:-
Coord C1 exon
chr3:3932537-3932799
Coord A exon
chr3:3931962-3932536
Coord C2 exon
chr3:3931623-3931961
Length
575 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CCCTCTTCCCTGCTCCTCAGGAA
3' ss Score
10.67
Exon sequences
Seq C1 exon
CTGCAGCGGAGCGTTCGTGGGCCAGCGATGCCAGGACCCCAGCCCTTGCCTCAGCACACCATGTAAGAATGCTGGAACGTGCTATGTTGTGGACCATGGCGGCATCGTGGACTATGCCTGCAGTTGCCCCCTGGGTTTCTCTGGGCCCCTCTGCCTGACACCTCTGGCCAATGCCTGCCTGGCCAACCCCTGCCGCAACGGGGGGACCTGTGACCTGCTCACTCTCACAGAATACAAGTGCCGGTGCCCGCCAGGGTGGTCAG
Seq A exon
GTAAGCTGTAGAAAGGCTGTGAACTTCACGGCTGGACCCTGAGGCCTGGGCCTACACTACTATTCGTGCTGGCTTGATATACTCTAGCACACCAAACTTTATCCTCCTGGCTCAGAGTTAAGCTGGGATCTAATATCCAGAAAAATCTTGGTGGTTCTTCAGGAACTCCGGTCCTTTCTGGCCCCAAACTATCTGATTTTTGGCTGCCCTATTCCAGGGCCCCAAACTCTCACTGTTTCTGTGAGTAAAGGGGCAGTTCTCATGTAGCCCTGGTCTTACCATCTCCCTGTCAGGGTCCCCCGAGCTGCCATTGCTCACATACGTGGGGTCCAGGAGACAGCTAGGTACAAGTTTTAGACGACTTTGCCTACTTTCTGTCCTTGGGCAGTGGCTTGGTCTCTTGTGACTTCCAGTCCTCTCTATGCAGACAGATGGCCACATTTTGCAGCAGGTACTGAGAATCATGAGGATAACACTTTAGGTCTATCCCTGGTTGGTGCCTCCGTGATGTCCAAATCTGCCATGAGCTCATCGGGAGGCCCTGGCTACAGCTGACCCTCTTCCCTGCTCCTCAG
Seq C2 exon
GAAAGTCATGTCAGCAAGCCGACCCCTGTGCCTCCAACCCCTGTGCCAATGGTGGCCAGTGCCTGCCCTTTGAGTCTTCATACATCTGTGGCTGCCCGCCCGGCTTCCATGGCCCCACCTGCAGACAAGATGTTAACGAGTGCAGCCAGAACCCTGGGTTGTGCCGTCATGGCGGCACGTGCCACAATGAGATTGGCTCCTATCGCTGTGCCTGCCGTGCCACCCACACTGGTCCCCACTGCGAGCTGCCCTACGTGCCCTGCAGCCCCTCACCCTGCCAGAACGGAGGCACCTGCCGCCCTACGGGGGACACCACCCACGAGTGTGCCTGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:3
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=WD(100=39.3),PF0000822=EGF=PU(90.6=32.6)
A:
NA
C2:
PF0000822=EGF=PD(6.2=1.8),PF0000822=EGF=WD(100=27.2),PF0764510=EGF_CA=WD(100=34.2),PF0000822=EGF=PU(81.2=22.8)
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:
CATCGTGGACTATGCCTGCAG
R:
CAATCTCATTGTGGCACGTGC
Band lengths:
356-931
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]