DreINT0105473 @ danRer10
Intron Retention
Gene
ENSDARG00000043130 | notch2
Description
notch 2 [Source:ZFIN;Acc:ZDB-GENE-000329-4]
Coordinates
chr8:19564405-19565080:+
Coord C1 exon
chr8:19564405-19564515
Coord A exon
chr8:19564516-19564887
Coord C2 exon
chr8:19564888-19565080
Length
372 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGT
5' ss Score
7.44
3' ss Seq
CTCTTTTTTTTTTGTTTCAGGGG
3' ss Score
12.1
Exon sequences
Seq C1 exon
GTGAGAACTGTCAGATTAACTATGATGACTGTGCCAGTAATCCCTGCCAGCACGGGACCTGTGAGGATGGAATCAATGAGTACAAATGCGTGTGCGAACCTGGATACACAG
Seq A exon
GTTTGTTCATCCCACATGCACAAATATAAATACACATATGCAGATGTGCTTCAGTCATTAAGTTCTGTGTAAATAGTTTGTAACACAACCACACAATGCATCTCTTCAATTTGATAAATCATACGTGTCAAACTCCAGTTCTGGAGGGCCACAGCCCCATACAATTTAGTTTTAACCGCAATGAAACACACCTGATCAAACTAATTAAGTCCTTCAGGCTTATTGTAGGTTTGTGTGTTGAAGCAAGGTTGGAACTTAACTCAGCAGGGTTGTGGCCCTTTAATAGCTGAGTATGACACCACTGATATATGATTGTGCTGCTTCAATCAACAGTGAAAGTTTTCATTATTCACTCTTTTTTTTTTGTTTCAG
Seq C2 exon
GGGAACGATGCGCTGATGAGATCAATGAGTGCAGTTCAAACCCATGTCAGAGTGGGGGGACGTGTGAGGATAAAGTGAATGGATTTAAGTGCAAGTGTCCAGTTGGGACTTATGGGCCCCTGTGTCTCTCAGGGGCAGACCGTTGTATCCGCATGCCCTGCCGGCATGGAGAGTGCATTGGGAAGCAGGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043130:ENSDART00000123104:12
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(6.5=5.3),PF0000822=EGF=PU(90.0=71.1)
A:
NA
C2:
PF0000822=EGF=PD(6.7=3.1),PF0000822=EGF=WD(100=47.7)
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:
GTCAGATTAACTATGATGACTGTGCC
R:
CTTCCTGCTTCCCAATGCACT
Band lengths:
294-666
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]