DreINT0105439 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65045209-65046073:-
Coord C1 exon
chr5:65045840-65046073
Coord A exon
chr5:65045320-65045839
Coord C2 exon
chr5:65045209-65045319
Length
520 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
ACCTTGCCTTGTGTCAACAGGAG
3' ss Score
9.85
Exon sequences
Seq C1 exon
GATACACAGGGCAGCACTGTGAGACAGATGTAGATGAGTGTCTGTCCAACCCGTGTCACTACGGCACCTGTAAAGATGGCCTGGCGTCCTTCACCTGCGTCTGCCGTGCGGGTTTCATGGGCCGTCTGTGCGAGATCAACATTAATGAGTGTCTCAGTCAGCCATGCCAAAACGGAGGCACCTGCCAGGACCGTGAGAATGCCTACTTGTGTGTCTGCCCCAAAGGAACTGCAG
Seq A exon
GTGCCACTTTTACTGTAATGGGGCAAATTATAAGTGTGTTTCAAGTCTTGATTTGAATGTGCCTACCGTTGGAGCACGTCTGATCATTTCTGGAAGCTGCTGGAAGCATTGTGTATTAAATGTGCTGAGTGGCATGGTGGCTCAGTGGTTAGCACTGTCGCCTCAGCAAGAAGGTCGCTGGTTTGAGTACTGAAAGTTGGCACATGTGTGGAGTTTGCATGTTCTCACCCTGTTCGAGTGGGTTTCATTCGGGTGCTCCGGTTTCCTCCACAGTCCAAAGACATGCGCTATAGGTGAATTGAATAAACTAAATTGGTCATAGTGTGAATGTGAGAGTAGATGGGTGTTTCCCAGTACTGGGTTGCGGCTGGAAGGGCATCTGCTGTGTAAAACATATGCAGGAATAGTTGGCGGTTCATTCCGCTGTGGCAGTCTTTGAAATAGAGACTAAGCCGAAGGAAATTGAATGAATGAATGAAATGTGCTATGTAAATAAACTTACCTTGCCTTGTGTCAACAG
Seq C2 exon
GAGCTAACTGTGAGATCAACCTGGATGACTGTCAGAGCAATCCCTGTGATTTCGGGAGATGCATCGACAAGATAAATGGGTACGAGTGTGCCTGCGAACCGGGATACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:11
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=6.3),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(93.1=71.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATACACAGGGCAGCACTG
R:
CTGTGTATCCCGGTTCGCAG
Band lengths:
345-865
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]