DreINT0105534 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53287561-53288685:-
Coord C1 exon
chr3:53288572-53288685
Coord A exon
chr3:53287675-53288571
Coord C2 exon
chr3:53287561-53287674
Length
897 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCTATGTTTGCCTGTCCCAGGGT
3' ss Score
6.98
Exon sequences
Seq C1 exon
GCTATCAGGGGAAGTACTGTGAGGTGGACATTGATGAATGCGAGAGCAACCCCTGCGTAAATGATGGCATCTGTCGAGATATGGTCAACGGCTTCACCTGCACCTGTCAGCCAG
Seq A exon
GTATGAAACATGTAACTCATAACACGTATATAGCAAAGCTCATTTATGTTGCCGCTTAATAGACGATTTCGACTCATTGTAATATCAGGCTAAATCCATTATGTCCCTCTAGCTTGATAGAGTTTTGTGTAATTACTCATTAGAGTGAGGTCTCAAGCACTATGCAACTGCGTGCCTGAACAAAGACACCATTGTGGCCTCTCTACACAAGCACCCCTCCTCTTCCCAACTTGTCCATAGAGAAGGGACAGCAGTCTCACCCGTCTCACTCTGCATAGAGGTGTGGGGGGGAACAGCAGCCCTGCTAATGAGATTCTTTTCCATGTCCGCAATTTACATCTGGGGCAGACAACCCCACACCCCCCATTTAGCTATTGAGCCGGTAGCGTTTGTGCATGGAAAGGGGGAGGGCCATTGGCCTTGAAGAAAACAATTCTAGCATCTCCCCCTTCTAACCTTCTGCCCTAGGCATCAACATAGATCCCATCATAACACTGTTAATCAACACAACACCCTCTAAAGATGCAGGAATGAACACTTCTGTGGGACACCAGACTTTTTTTGTACTTACTAGCATATTTTCACAGACAGGGTTTAAGGCCTCCTGCAAGCTCAGTGCCTACACAAGTGCACATTTTTTCAGATAATGTAATTTAATTGATGGCAGAAATGTATGAAAAGCTAATTAACATCCAAAAATGGACAGTTAACATTCATTTGCTATAACATACAGATTGAGATGTATAGATTTTAGCTTTAAATAAAGCAAGGTGCAGATATCTTCTACTTGGCTAAGCCCTACTGCCCCTAAAGCTGAACCTAATGACCCAACCAGTGTGAGGAGCTCACCTCCGCTGCCTTAGACTGACCCCTAACCTCTATGTTTGCCTGTCCCAG
Seq C2 exon
GGTTTACTGGCACCATGTGTCAAATCGACATTGATGAGTGCGCCAGCACTCCTTGCCAGAATGGAGCCAAGTGCATTGACCGACCTAATGGATATGAATGCCGCTGTGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:9
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(16.1=12.8),PF0000822=EGF=PU(83.3=64.1)
A:
NA
C2:
PF0000822=EGF=PD(13.3=10.3),PF0000822=EGF=PU(80.6=64.1)
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:
AGGGGAAGTACTGTGAGGTGG
R:
CTTCAGCACAGCGGCATTCAT
Band lengths:
222-1119
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]