DreINT0105524 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53277739-53278325:-
Coord C1 exon
chr3:53278157-53278325
Coord A exon
chr3:53278044-53278156
Coord C2 exon
chr3:53277739-53278043
Length
113 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGA
5' ss Score
6.69
3' ss Seq
CAACTTTTATTTTACTATAGATG
3' ss Score
7.06
Exon sequences
Seq C1 exon
GTGGAAGAACCAAGCATTCTGTCAGATGGTGAGGATGCAGTTGACAGCAGACAGTGGACACAGCATCACTTGGCAGCAGCAGATATCCGCATGCCACCTTCCATGGCACTTACACCACCACAAGGAGAGTTTGACAGTGACTGCATGGATGTTAATGTCAGAGGCCCTG
Seq A exon
GTATGATACGTTTATCTACTGTTTGAAGTCCAGCTGTCCCTTCTTCTTGGATATTTCTTAAAGAAGAATAGCAAATGAACTTAAAACATTTGCCAACTTTTATTTTACTATAG
Seq C2 exon
ATGGCTTCACACCTCTGATGCTGGCATCTTTCTGTGGAGGAGGGCTTGAGCCAGAGGTGACCGAAGATGATGACTCAGATGAATCCTCAGCCAACATCATATCTGACCTCATTTACCAGGGAGCATCACTTGCAGCTCAAACTGACCGCACTGGAGAGACTGCTCTGCACCTGGCTGCACGCTATGCCCGGGCAGATGCAGCTAAAAGACTCCTGGATGCTGGGGCTGATGCAAATGCACAGGATAACACAGGTCGCTCACCTTTGCATGCAGCTGTGGCAGCTGATGCACAGGGAGTTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.737 A=NA C2=0.275
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF127962=Ank_2=PU(83.3=73.5)
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:
GATATCCGCATGCCACCTTCC
R:
CTCCAGTGCGGTCAGTTTGAG
Band lengths:
244-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]