RnoINT0102283 @ rn6
Intron Retention
Gene
ENSRNOG00000004346 | Notch3
Description
notch 3 [Source:RGD Symbol;Acc:620761]
Coordinates
chr7:14165352-14166334:-
Coord C1 exon
chr7:14166216-14166334
Coord A exon
chr7:14165918-14166215
Coord C2 exon
chr7:14165352-14165917
Length
298 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TCCCCTCACCCCACCATTAGCCA
3' ss Score
4.17
Exon sequences
Seq C1 exon
GGCCTCGATGTCAGACTGCTCTGTTCCCCTGTGAGTCCCAACCGTGTCAGCATGGAGGCCAGTGCCGTCCCAGCCTAGGCCGTGGAGGTGGGCTGACCTTCACCTGTCACTGTGTCCAG
Seq A exon
GTAGGTGTGACTGGTGGGGAAAGAGAAGGCAGGTGGCTTCAGGGAGGTGTATGTGTGTAAGGGAAAAGTGGAAGGCAAAGAGGTTCTGAGACGGTGAATTGTAGTTTGGAGTGTAACTTAGTGAAATCGTGACCTGGCTTTCTGTAGAGGAAAGGGGAGGTTGCTGGAATTGGAGAGGTTGGGAGAGGGAGGGTCATCATTTCTCAAGTCTTGACCTCCACTCTTCTCTGTCTTTTCCACCCATCTGTTTCTTCTCACTACCAATTTTTCTCTTTCTGTCCCCTCACCCCACCATTAG
Seq C2 exon
CCATTCTGGGGTCTGCGTTGCGAGCGGGTGGCACGCTCCTGCCGGGAGCTGCAGTGCCCAGTGGGTATCCCATGCCAGCAGACAGCCCGTGGGCCGCGCTGTGCTTGTCCTCCCGGGCTGTCTGGGCCCTCCTGCCGGGTTTCTAGGGCGTCACCCTCTGGAGCTACTAACACCAGCTGCGCTGCTACTCCTTGTCTGCATGGGGGCTCCTGCCTACCTGTACAGAGTGTCCCTTTCTTCCGCTGTGTATGCGCTCCGGGCTGGGGTGGCCCGCGTTGCGAGACCCCTTCCGCAGCCCCTGAGGTCCCTGAGGAGCCACGGTGCCCGCGAGCCGCCTGTCAGGCCAAGCGAGGGGACCAGAACTGCGACCGTGAGTGCAACAGCCCAGGCTGTGGCTGGGACGGCGGTGACTGCTCGCTGAATGTGGACGACCCCTGGAGGCAGTGTGAGGCACTGCAGTGCTGGCGTCTCTTCAACAACAGCCGGTGCGATCCAGCCTGCAGCTCTCCTGCCTGCCTCTATGACAACTTTGACTGCTACTCTGGTGGCCGCGACCGCACCTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004346:ENSRNOT00000037456:23
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:
PF126612=hEGF=PD(23.1=7.5),PF0000822=EGF=PU(80.6=72.5)
A:
NA
C2:
PF0000822=EGF=PD(13.9=2.6),PF0000822=EGF=WD(100=17.5),PF0006612=Notch=WD(100=19.6),PF0006612=Notch=WD(100=19.6),PF0006612=Notch=PU(12.8=2.6)
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:
TGTCAGACTGCTCTGTTCCCC
R:
CGCAGCTGGTGTTAGTAGCTC
Band lengths:
292-590
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]