DreINT0105434 @ danRer10
Intron Retention
Gene
ENSDARG00000103554 | notch1a
Description
notch 1a [Source:ZFIN;Acc:ZDB-GENE-990415-173]
Coordinates
chr21:4623205-4623733:-
Coord C1 exon
chr21:4623549-4623733
Coord A exon
chr21:4623338-4623548
Coord C2 exon
chr21:4623205-4623337
Length
211 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAA
5' ss Score
5.13
3' ss Seq
CTGTTCATCATCTCCCTCAGTGC
3' ss Score
7.78
Exon sequences
Seq C1 exon
GTGTGTCTGTGGCAGTTTTGTGTCGTCATGCGGGTCAGTGTGTTGATGCAGGAAACACACACCTGTGCAGGTGTCAGGCTGGATACACCGGCAGTTACTGTCAGGAGCAGGTGGACGAGTGTCAGCCGAACCCCTGCCAGAATGGAGCCACGTGCACAGACTATCTGGGAGGATACAGCTGTGAG
Seq A exon
GTACAAACACACACACTCACACACATTTAGCAGACGCTTTTACCCAAAGTGACTTACATCCATACTCTCGCGCACACACACTCTCTCACACACACACACACACAGGTTTGTTTTTGTGGATTGTGGGGACATTCCATAGGTTTTCATTGTTTTTCCTTTAGTTCAGTTTGTTCTTATTGGATTCTTAACATCTGTTCATCATCTCCCTCAG
Seq C2 exon
TGCGTTCCTGGATATCATGGTATGAACTGCAGCAAGGAGATAAACGAGTGTCTTTCTCAGCCCTGCCAAAATGGAGGAACCTGCATCGACCTCGTGAACACCTACAAATGCTCCTGCCCACGAGGAACACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103554:ENSDART00000158232:7
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=WD(100=43.5),PF0000822=EGF=PU(67.7=33.9)
A:
NA
C2:
PF0000822=EGF=PD(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGGCAGTTTTGTGTCGTCA
R:
GGGCAGGAGCATTTGTAGGTG
Band lengths:
297-508
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]