DreINT0105522 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53278426-53278839:-
Coord C1 exon
chr3:53278611-53278839
Coord A exon
chr3:53278517-53278610
Coord C2 exon
chr3:53278426-53278516
Length
94 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
ATATTTAATACTCTTTACAGACA
3' ss Score
6.29
Exon sequences
Seq C1 exon
GTGAAAAAAGAGAGCCCTCGATTACTGAGATACCCGAATGGGCTAGGCTACTGCTAGTAGGTGTAGCTTCTCTCTTCTTGTTAGTAATCTTGATGGTTGGCATGTTGATTGCCCGCCGCAAGCGTGAACACAGCACACTCTGGTTCCCTGAGGGCTTCTTCCTCAAAAAGGAAACAAGCAGTAACAAGAACCGCAGAGAACCTGTGGGCCAAGATTCACTGGGCATGAA
Seq A exon
GTGAGTTGGTCATGCAGTTTTTTGATTATAGCTATTATCAGTATGGTTCACTGAAACTTCAAAGGCACTAACTAATATTTAATACTCTTTACAG
Seq C2 exon
ACACATGCCAAAGACAGTGGAAGAGTCTCTTCTGGCTGATCACAGTGACCAGTGGATAGATACAGACTGCCCAGAGGCTAAGCGACTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.247 A=NA C2=0.258
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(14.3=11.7)
A:
NA
C2:
NO
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:
GTTCCCTGAGGGCTTCTTCCT
R:
TTAAGTCGCTTAGCCTCTGGG
Band lengths:
177-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]