DreINT0105477 @ danRer10
Intron Retention
Gene
ENSDARG00000043130 | notch2
Description
notch 2 [Source:ZFIN;Acc:ZDB-GENE-000329-4]
Coordinates
chr8:19568741-19569261:+
Coord C1 exon
chr8:19568741-19568860
Coord A exon
chr8:19568861-19569108
Coord C2 exon
chr8:19569109-19569261
Length
248 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
TGTCTGGTATGTGTGTGCAGGAG
3' ss Score
6.9
Exon sequences
Seq C1 exon
GGAAACACTGTCTGGAGAAGTTGATCCCATGTGCCTCTCAGCCCTGTCAGAGACGAGGAGTCTGTCAGCCATCGCTGGATTACACCAGCTACACCTGCAAATGCCACAGCGGCTGGGAGG
Seq A exon
GTGAGCGCTTCAAGTCTGGGTGTTGGTGTGATTACATATTTAAGTCAGTTAAATGTCTGTTGAAGGAACAGTATCAATAGATATTAAGCTGACAGTCTACTAATACTTAAATGGACCATCAAAATAAAGTGTTTCTCATATTTGATCTGAGACGATCACATATAAACTTTTCCTTGATAAAACATGATGTGAGCTGTGGACATCTATTAAAAGTGTCTGAAGGGATTTTGTCTGGTATGTGTGTGCAG
Seq C2 exon
GAGCCCAATGCACAGAGGATAAAGACGAGTGTAAGAAGAGCCCTTGTCAGAATGGTGCTCGCTGTGTGAATATAGTTGGCAGCTACCGTTGCGAATGCCCGCCTGGATACAGCGGGGACAACTGCCAGACCAACATCGATGACTGCAGCTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043130:ENSDART00000123104:16
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=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0000822=EGF=WD(100=65.4),PF0000822=EGF=PU(9.7=5.8)
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:
GGAAACACTGTCTGGAGAAGTTGA
R:
AGCTGCAGTCATCGATGTTGG
Band lengths:
270-518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]