DreINT0105506 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53285646-53286055:-
Coord C1 exon
chr3:53285945-53286055
Coord A exon
chr3:53285839-53285944
Coord C2 exon
chr3:53285646-53285838
Length
106 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
TGACCGTCCCTTCTTTTCAGGAC
3' ss Score
12.6
Exon sequences
Seq C1 exon
GTACCAACTGTGAAATCAACTTTGACGACTGTGCTAGCAACCCTTGTGACTACGGAATTTGCAAAGATGGCATAAATCGCTATGAGTGTGTCTGCAAACCTGGCTTTACCG
Seq A exon
GTGAGATGGGTGGAACACCCACCTTAATCATTTTAAACAATCACAAGAGTTGGCAAATTCACAAATGCAAAAGAGAAATCACATTTTGACCGTCCCTTCTTTTCAG
Seq C2 exon
GACCTCAATGTAAGGATGAGATAGATGAGTGCCAGTCGAATCCCTGTCGCAATGGAGGGACCTGTGTAGATGATGAGAATGGCTTCCACTGTCAGTGCCCTGAAGGGTTCCATGATCCCTACTGCTATTCACAAGTGGATGAGTGTGCCAGCAATCCATGTTTACATGGGACCTGCAGGGATGACCCTAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:12
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=5.3),PF0000822=EGF=PU(90.0=71.1)
A:
NA
C2:
PF0000822=EGF=PD(6.7=3.1),PF0000822=EGF=WD(100=47.7),PF0000822=EGF=PU(53.3=24.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGACGACTGTGCTAGCAACC
R:
GATTGCTGGCACACTCATCCA
Band lengths:
246-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]