DreINT0105492 @ danRer10
Intron Retention
Gene
ENSDARG00000043130 | notch2
Description
notch 2 [Source:ZFIN;Acc:ZDB-GENE-000329-4]
Coordinates
chr8:19557635-19558572:+
Coord C1 exon
chr8:19557635-19557900
Coord A exon
chr8:19557901-19558233
Coord C2 exon
chr8:19558234-19558572
Length
333 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
TGCTGATGTTTACTCTTCAGGTC
3' ss Score
8.84
Exon sequences
Seq C1 exon
GTGTGCTCCTGGTTTCTTAGGGGAGTACTGTCATCACAGTGACCCTTGTAATCTGTTGTATTGTAAAAATGGAGGAGAGTGCAAGGTGAGCGTGGCCGGTGTCCCTGGGAGCCCCTCATGCGTGTGTCCTCTGGGCTTTGCGGGTGAGCACTGCGAAATCCAGAAAAACTCCACCTGCTACCCCAATAACCCTTGCACCAATGGAGGAAAGTGCTTGCTCCTTCCCAACGACCAATACAAATGCCAGTGTGCCCTTGGGTGGACAG
Seq A exon
GTCAGATCTCTCTCTTAATCTTTTCTTTTCATAATCATAAAAACAACAATAAAACAGCTCTGTTATAGACCATTTCAATGTTGTGATGTCATTAGGCCATGAACACTTCCTGCTTGTTATCAAACTATTTCATAACAATTAAACCATGACTTAATGTTAAAACAGCTATCATAACATTATTTATCAGTGTGTGGCTCTTTTTGTATTCTCGTAAGCTATAGCAACTAAAAATGTAAAACAGGAAATACGTTGGGACCATTGTTTTTGTTTACATCCCACAAAATGGTCTGTAGTTTGAATTGACTTTGTCTTATGCTGATGTTTACTCTTCAG
Seq C2 exon
GTCAGCATTGTGAGCAAGAGGACGCATGTCTGTCCAGCCCATGTGCCAACAAGGGTATATGCAATGCTCTGCCAAATCGCGAATACTCTTGTACCTGTGCGCCTGGTTTTCATGGTTCCCGTTGTCTTAACGACACAGACGAGTGTGTGGACCCGTTAGTATGTAAGAACAAAGGCGTTTGTGTGAACACCATAGGCTCATATCGATGCAACTGCCAACCTGGCTTCACCGGATTGGACTGCGGGAGTCCTTACTTCCCCTGCTCTCCGTCCCCCTGCCAAAATGGTGGGACCTGCCGGCAAACAACAGAAACCACCTATGTATGCCACTGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043130:ENSDART00000123104:3
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(27.3=10.0),PF0000822=EGF=WD(100=38.9),PF0000822=EGF=PU(90.9=33.3)
A:
NA
C2:
PF0000822=EGF=PD(6.1=1.8),PF0000822=EGF=WD(100=28.1),PF0764510=EGF_CA=WD(100=38.6),PF0000822=EGF=PU(81.2=22.8)
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:
CCCCAATAACCCTTGCACCAA
R:
AGCAGGGGAAGTAAGGACTCC
Band lengths:
350-683
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]