DreINT0105474 @ danRer10
Intron Retention
Gene
ENSDARG00000043130 | notch2
Description
notch 2 [Source:ZFIN;Acc:ZDB-GENE-000329-4]
Coordinates
chr8:19564888-19566938:+
Coord C1 exon
chr8:19564888-19565080
Coord A exon
chr8:19565081-19566792
Coord C2 exon
chr8:19566793-19566938
Length
1712 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TTCAACTGTTTTCTGTGTAGGTA
3' ss Score
10.17
Exon sequences
Seq C1 exon
GGGAACGATGCGCTGATGAGATCAATGAGTGCAGTTCAAACCCATGTCAGAGTGGGGGGACGTGTGAGGATAAAGTGAATGGATTTAAGTGCAAGTGTCCAGTTGGGACTTATGGGCCCCTGTGTCTCTCAGGGGCAGACCGTTGTATCCGCATGCCCTGCCGGCATGGAGAGTGCATTGGGAAGCAGGAAGG
Seq A exon
GTAAGAACTGACTTAATTTGCAAGCAATTTTGTCCATGCATCAATTCTTTTTTAATGTTTATTAACATTGATACAACATATAATAACATACAATAACATACATTTAAAACATACACATACACAAAATTCATACACATCAACACCAAATGATTTTACAAATATTGTGTAAACATGCCAAAATGCATTTTTATGAATTCATGACAGGTTCACACTGCAACGAGAGTCACTATAATGTGTATTATTATAAAGCCAGGGCCCTGTGAAATTTATTTTATTTTATTATATTTTATTTACAGTTTAACTTTTTTCTTAGGTTTTGTTGAATTTTTCCTGAATTCCTGTTTAAATTTTCCTGAATTACATTATTTTTATTGTTCCAGGGCTTTTGGGCCCTACCATGCACCCAGCTTAATAAGGCCCAAGACATGTTTTGCGTGAATTGTTGCAATTTACATACCAACGCAATCCTAATATTCACATTTTGCGCCACGTTGTTTAAGTATCAAATCCATTTGCACTACTTTGACTAGTGAGCCGGTCAATAAAGAAGGTGTGTTGAGGCGCATTGTTGGCATGTTACTATTTTGAGAAAGTTAAATAAACCATGCAACTGACCAAGTAAAACCTGGCTAAAGTTAGTTATGCGCCTATCAAACGCTTGATACACACAGGATGTACAGCAATAAACAAATATCTTTACATATAAAAAATCTTAACAAATGAAAATATCTTTACATATAAGCTTTTTTCAGTTTATTCATGACAATTAGCATTTTTATTATAGTGTTGCTATTATTAGCCGTATTACTTATTATATGCATATTTATGTATATATTTTTTAAAATAAAAACAAGATTTGTCCACCTGTTGGGTTTTTTTGACGTCTGCATCACCAAATGGGGCAAAAAAATAGTAACTTTGCAATATGACATTGTGATATGTTGTTTTTGAGCACACTTTGTTATTATTGTTCATTTATTACTTTGCTGGAAATTAGAGCTGAATTTAGAAATAGTTTTGAAACAAATCTTTGCTCTTGACAAACAAAATTAAATATGTTGGCTAATGAATGCCTTCCGTGGAGTGCGTACAACACCGTTGACTTATTCATAAAAGCAAAGAAAAGACCGCATGGAAGAGGCTCGTTCTTTATCCTCGCTCTGCAGATGGTTTGTTTAACGGTTTTCTGGCTAGTGAAGCATTCAGTTTGTCCATTCAGTTTTTCTTCTTACAAAGTCTGCCATGTTAATAAATAGCAAATGCACAACGGAGTGACGCAACTGAATTTTAAGGGAATGAGAGATAACACCCCCATTGGTTTAATACATGTTATGTGCAAAACACACCCATAACTCATAATGAGAATAAGCACAACCCTGTTAGACCATGCGCCGCGGCGCAAATTGTATTTTTCCATCCTTAAAATAGCAAAAAAGGATTTAGACACTCCCTTAATGCTTTTGCTCCATGCACTTTAGACTTTGCGCCTAGATCATTAAAATAGAGCCCTTTGTGTTTTTATATTTCCAGGCAAAGTTCTGTGTCATGATTTGTTTAGGTGTAGTAGCATTCGTTTAAATTATTTGTCCAAAATATAACAAATGCTGTGTTTTGTGAGCTTATTATAAGGAACTATTATATGTTTAAATATACAGTATAAATCCTCCTCAGTGGCCTTTGTTCCTTACTATTTTCAACTGTTTTCTGTGTAG
Seq C2 exon
GTATCTTTGTCAATGTGAGCCAGGCTGGGAGGGTACGAACTGTGACCAAGAGAAGAACGAGTGTCTGTCCAACCCGTGTCAGAATGGTGGAACCTGTAATGACCGTCTGAATGATTATACCTGCGTATGCGCCCGTGGGTTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043130:ENSDART00000123104:13
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(6.7=3.1),PF0000822=EGF=WD(100=47.7)
A:
NA
C2:
PF126612=hEGF=WD(100=26.0),PF0000822=EGF=PU(93.3=56.0)
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:
GGAACGATGCGCTGATGAGAT
R:
CAAACCCACGGGCGCATAC
Band lengths:
335-2047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]