DreINT0105520 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53278932-53279563:-
Coord C1 exon
chr3:53279240-53279563
Coord A exon
chr3:53279081-53279239
Coord C2 exon
chr3:53278932-53279080
Length
159 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
ACTCTTTGGCTTCTCTGCAGGTC
3' ss Score
10.17
Exon sequences
Seq C1 exon
CCCCATCTATGAAGCATACTGCACTGACCATTATGCAGATGGACTCTGTGATCAAGGATGCAATACTGAAGAATGTGGCTGGGATGGACTGGATTGTGCAAGGAAGATTCCAGAAGACCTTGCTGAAGATATGCTTGTTATTGTAGTCCTACTGCCCCCAGAGGAGCTTCTAAGGACACAAACAGCTTTCCTGCAGAAACTAAGTGCCATCCTACGCACCACGTTGCGCTTCCGTCTCGATCGAAATGGAGATTACATGATCCGACCTTACACAGGCCGTGAGACGCGCATTAAACGGGAGCTTAATCCTCAGGAGGTCATTGG
Seq A exon
GTGAGTTGCAGAAAAAAAAACTACTTCACATACATTTTCATATTGTCAAAATAACACAGGTTAAATGTAATAATCTCAGCAGGAACCTGAATGATCAAGAATTGCGTTCTCTGCACAGATTTGGGAGTTTTACACTTTTACTCTTTGGCTTCTCTGCAG
Seq C2 exon
GTCCATTGTATATTTGGAAATAGACAACAGGCTGTGCTCTCAGGGCTCAGATGACTGCTTCCGCAATGCTGACAGTGCTGCTGAATACCTTGGTGCTCTGTCTGCTCGGGAGATGTTGCGCTTCCCATACCCCATTAAAGAAGTGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:25
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:
PF0006612=Notch=PD(82.5=30.3),PF068168=NOD=WD(100=52.3),PF076847=NODP=PU(4.8=2.8)
A:
NA
C2:
PF076847=NODP=FE(79.4=100)
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:
GTAGTCCTACTGCCCCCAGAG
R:
AAGCAGTCATCTGAGCCCTGA
Band lengths:
242-401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]