RnoINT0102270 @ rn6
Intron Retention
Gene
ENSRNOG00000004346 | Notch3
Description
notch 3 [Source:RGD Symbol;Acc:620761]
Coordinates
chr7:14176456-14176970:-
Coord C1 exon
chr7:14176737-14176970
Coord A exon
chr7:14176567-14176736
Coord C2 exon
chr7:14176456-14176566
Length
170 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTAT
5' ss Score
4.29
3' ss Seq
TTCCTCCTCCCCTGTTGTAGGTG
3' ss Score
11.11
Exon sequences
Seq C1 exon
GCTTTGAGGGCACCCTGTGTGAGCGAAACGTGGACGACTGCTCTCCGGATCCCTGTCACCACGGGCGGTGTGTCGACGGCATTGCTAGCTTCTCATGCGCTTGTGCGCCAGGCTACACGGGCATACGCTGCGAGAGCCAGGTGGATGAGTGCCGCAGCCAGCCCTGCCGATACGGGGGCAAATGTCTAGACTTGGTGGACAAGTACCTCTGCCGCTGTCCTCCCGGAACCACAG
Seq A exon
GTTTATTTTATTTTGTTTTTTTGGGTTTTTTTTTTTTTTTTTTGTTTTTTGTTTTTGAGGGGACTGGGCTCTGACAGTACATGGGGGTGTGTGGGTGTCCGTGATGAGTTTGCAAGGGTTGCTTGATGATAGCCCTTACTCCTGCCATACTTCCTCCTCCCCTGTTGTAG
Seq C2 exon
GTGTGAACTGCGAAGTCAACATCGATGATTGCGCCAGCAACCCCTGTACCTTTGGAGTTTGCCGTGATGGCATCAACCGCTATGATTGTGTCTGTCAGCCTGGATTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004346:ENSRNOT00000037456:11
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(16.1=6.3),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(90.0=71.1)
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:
GAAACGTGGACGACTGCTCTC
R:
TGGCGCAATCATCGATGTTGA
Band lengths:
246-416
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]