DreINT0105526 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53277427-53278043:-
Coord C1 exon
chr3:53277739-53278043
Coord A exon
chr3:53277575-53277738
Coord C2 exon
chr3:53277427-53277574
Length
164 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
CCATGATTTTGCATCTTTAGATT
3' ss Score
7.85
Exon sequences
Seq C1 exon
ATGGCTTCACACCTCTGATGCTGGCATCTTTCTGTGGAGGAGGGCTTGAGCCAGAGGTGACCGAAGATGATGACTCAGATGAATCCTCAGCCAACATCATATCTGACCTCATTTACCAGGGAGCATCACTTGCAGCTCAAACTGACCGCACTGGAGAGACTGCTCTGCACCTGGCTGCACGCTATGCCCGGGCAGATGCAGCTAAAAGACTCCTGGATGCTGGGGCTGATGCAAATGCACAGGATAACACAGGTCGCTCACCTTTGCATGCAGCTGTGGCAGCTGATGCACAGGGAGTTTTCCAG
Seq A exon
GTAAAGTCATGGCCTTAAGAATAACTTTTTTTTTTTAAATAGACTACTGTAAATAGTAGATTATGAGGCTATGTATTTTATTCTGACGTATGGTATATTTGAATGTTACTAATGTTATAATAAGGTGATGTATCCTGATGTATACCATGATTTTGCATCTTTAG
Seq C2 exon
ATTCTGATCAGGAACCGTGCCACAGACTTGGACGCGCGCATGTATGATGGCTCCACTGCTCTGATACTTGCAGCCCGTCTGGCAGTAGAGGGCATGGTGGAAGAGTTGATCACCTGCCATGCTGATGTTAATGCTGTTGATGAAATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.275 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(83.3=73.5)
A:
NA
C2:
PF127962=Ank_2=PD(14.4=26.0),PF127962=Ank_2=PU(31.2=58.0)
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:
CGGGCAGATGCAGCTAAAAGA
R:
TCAGCATGGCAGGTGATCAAC
Band lengths:
242-406
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]