DreINT0105515 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53282218-53282666:-
Coord C1 exon
chr3:53282482-53282666
Coord A exon
chr3:53282351-53282481
Coord C2 exon
chr3:53282218-53282350
Length
131 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TGGCATGTTTATTTCTCCAGTGT
3' ss Score
6.4
Exon sequences
Seq C1 exon
GCCGCCAGACAGATGAGCTTTGCCTTCACGGTGGACACTGTGTCAACACTGGCAACACGCACTACTGCAAATGTCCGGCAGACTACACAGGCAGTTACTGCGAGTCTCAGTTTGACCACTGTGAGGAAAAACCTTGCCTCAATGGCGCCACCTGCAGAAGCTACATGGGAGGATTTACTTGTGAT
Seq A exon
GTAAGTAATCTTGCCACAGTTACTAATACCACATACCTTTTTTTATAATAGTATAATGACAAATTACCTACATAGTATGAAGTTCTGAAGACTGAAGAGTAGATGTTAAAATGGCATGTTTATTTCTCCAG
Seq C2 exon
TGTATGCCTGGTTATGAGGGAAACAACTGTGAGAGAGAGGTCAATGAGTGCCAGTCTCACCCATGTCAGAATGGAGGAACCTGCATCGACTTAGTGGGACATTACATCTGCTCCTGCCCTCCAGGAACACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:20
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=48.4),PF0000822=EGF=PU(67.7=33.9)
A:
NA
C2:
PF0000822=EGF=PD(25.8=17.8),PF0000822=EGF=PU(84.8=62.2)
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:
GACACTGTGTCAACACTGGCA
R:
TCCCACTAAGTCGATGCAGGT
Band lengths:
251-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]