RnoINT0102274 @ rn6
Intron Retention
Gene
ENSRNOG00000004346 | Notch3
Description
notch 3 [Source:RGD Symbol;Acc:620761]
Coordinates
chr7:14172736-14173685:-
Coord C1 exon
chr7:14173572-14173685
Coord A exon
chr7:14172892-14173571
Coord C2 exon
chr7:14172736-14172891
Length
680 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAC
5' ss Score
7.56
3' ss Seq
GCTTCCCCTCTCGCCTCCAGGCC
3' ss Score
10.14
Exon sequences
Seq C1 exon
GTCATCAATGTGAGGTGCTGTCCCCCTGCACTCCAAGTCTCTGTGAGCACGGAGGCCACTGTGAGTCTGACCCTGACCAGCTGACTGTCTGTTCCTGTCCTCCAGGCTGGCAAG
Seq A exon
GTACACCAGTGTCCTCCTCCTCTTCCTTCTCTTCTCCTTCCTCTCTCTTTTTTATTTTTAAAGATTTATTTATTTAATGTATATAAGCACACTGTTACTGTCTTCAGACACACCAGAAGAGGGCACCAGATCCCATTTCAGATGGCTGTGAGCCCCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGCGCTCTTAACCTCTGAGCCATCTCTCCAGCCCCCTCCTTCCTCTCTTTTTCTCCCCTTCTTCCTCCTCTTCTGCACTTTGCTCCATATTGGGTAGCCCAGGGAGCCCAGAATGGACTCAATCCCTCTCTGCCTTTGAAGGTGCTTCATTCTGGGAAAAGACAGCTGGGTCCAGACATTCCCAGCCCATCGGAGTCAGCGCAGGATAAGAGGGAGCCATCTGGGGCTGAGGATGCTGGGATACCTGAGATTTGATGACAGGTTTTTGAAGGGGTGACTTCAGACTGTGTATTCAACAACTAGAGAGACAGGCTAAACAGACAGGCGGAATATAGTTCAGAAGTGGCCTGTGCCAAATGCCTAGAGTCAGCGGCTTGTCTTTGCCCTTCCTTGCCTCAGCCTATGGGTTTTTGAGCTGCAGGCATCCTCGGATCCCATTTTACCCCTTTAACCTCAATTGCTTCCCCTCTCGCCTCCAG
Seq C2 exon
GCCCTCGATGCCAGCAGGATGTGGATGAATGTGCTGGTGCCTCACCTTGTGGCCCCCATGGTACCTGCACCAACCTGCCAGGGAGCTTCAGGTGCATCTGCCATGGAGGATACACTGGCCCTTTCTGTGATCAGGACATTGACGACTGTGACCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004346:ENSRNOT00000037456:15
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(90.6=74.4)
A:
NA
C2:
PF0000822=EGF=PD(6.2=3.8),PF0764510=EGF_CA=WD(100=73.6),PF0000822=EGF=PU(9.7=5.7)
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:
GTCATCAATGTGAGGTGCTGTC
R:
TGGGGTCACAGTCGTCAATGT
Band lengths:
270-950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]