DreINT0105509 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53283664-53284139:-
Coord C1 exon
chr3:53283906-53284139
Coord A exon
chr3:53283817-53283905
Coord C2 exon
chr3:53283664-53283816
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
AAATGCCTTCCAAACCACAGGCC
3' ss Score
4.8
Exon sequences
Seq C1 exon
GTAACTTATGTCAGGTGAACATCAATGAGTGTGCCTCCAGCCCCTGTCTAAATCAGGGCACCTGTGTGGATGGAGTTGCTAGTTTCACCTGTCTCTGTGAACCACCTTATAGTGGACCCACTTGTGCAGAACTGCTCACACCTTGCTCTCCCAACCCCTGTGCCAACCATGCTTCCTGCGTGCACACACCTGACTACCTAGGCTACCAGTGTAACTGCCAACCAGGCTGGCAAG
Seq A exon
GTAAGTTATTATATTCACATATTAGTTCATGTTCAAAAGAATTGGTTTGCCTTTAGTATGTCTAACTCTAAATGCCTTCCAAACCACAG
Seq C2 exon
GCCATTTGTGCAACAATGACATCAATGAATGCACCTCTAACCCGTGTAAGAACCGTGGGACTTGCACAAATACCCTTGGAGGCTATGTGTGCTCCTGCCGTGCTGGCTACACTGGACCCAATTGTGAAACTGATATCAATGACTGCTCGCCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:15
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(3.3=1.3),PF0000822=EGF=WD(100=39.2),PF0000822=EGF=PU(90.9=38.0)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0000822=EGF=WD(100=59.6),PF0000822=EGF=PU(9.7=5.8)
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:
CTCACACCTTGCTCTCCCAAC
R:
ATTTGTGCAAGTCCCACGGTT
Band lengths:
171-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]