DreINT0105505 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53285945-53286376:-
Coord C1 exon
chr3:53286143-53286376
Coord A exon
chr3:53286056-53286142
Coord C2 exon
chr3:53285945-53286055
Length
87 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTGTTTGATTCCCACAAAGGTA
3' ss Score
5.22
Exon sequences
Seq C1 exon
GTTTTGAAGGAAGACTGTGTGAGAGCAACATTGATAATTGTAAGCCTGACCCATGCCACCATGGTACTTGCGTAGATGGCATTGCCAGTTATACTTGCAACTGTGAGCCTGGCTACACTGGCTATCGCTGCGAAAACCAGCTCAATGAGTGCCATAGCAACCCCTGCCAGAATGGTGGCAAATGTGTTGACCTTGTCAACAAATACATCTGCCAGTGTCAACATGGCACTTCAG
Seq A exon
GTGAGGAATTATGTATTACAGATTCATCTGCATTGGCTATATCATTTTTACACCATTTCTTAATAACACTGTTTGATTCCCACAAAG
Seq C2 exon
GTACCAACTGTGAAATCAACTTTGACGACTGTGCTAGCAACCCTTGTGACTACGGAATTTGCAAAGATGGCATAAATCGCTATGAGTGTGTCTGCAAACCTGGCTTTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(16.1=6.3),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(90.0=71.1)
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:
CAACTGTGAGCCTGGCTACAC
R:
GGTTGCTAGCACAGTCGTCAA
Band lengths:
179-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]