DreINT0105423 @ danRer10
Intron Retention
Gene
ENSDARG00000103554 | notch1a
Description
notch 1a [Source:ZFIN;Acc:ZDB-GENE-990415-173]
Coordinates
chr21:4612199-4613238:-
Coord C1 exon
chr21:4613028-4613238
Coord A exon
chr21:4612281-4613027
Coord C2 exon
chr21:4612199-4612280
Length
747 bp
Sequences
Splice sites
5' ss Seq
CAAGTCAGT
5' ss Score
2.74
3' ss Seq
GTGACTCTGTGTTCCATCAGGCC
3' ss Score
8.82
Exon sequences
Seq C1 exon
GTGAAGGTGGTCCCCCAAAGACTGGTGAGATGTACCCCATGTTCCTGGTCCTGCTGGCTCTGGCTGTTCTGGCTCTGGCCGCTATCGGTGTGGTCGTCTCCAGGAAGAGGAAGCGGGAACATGGCCAGCTTTGGTTCCCCGAGGGATTTAAAGTCAACGAACCCAAAAAGAAGAGGAGAGAACCAGTGGGAGAGGACTCTGTCGGACTCAA
Seq A exon
GTCAGTTTCCACACACTTGCATGAGAGCTCTATATATTAATGCCATATATTCTGCTTTGGTTAGCTCTTTAATTTAAGCCGGTTTTATTTGTATTTATTGCTTTTTTTAGTTGTTATTGATATTGTAAATCTGCTTTAGGTCAAGACATTTTTATTTCTGTAACACTTTTATCATGTAGATGGTGTCAAAGCAGCTTGACATAGATGAAGAATAAAAGTGTAAAAAGCCATAACAAATATTTATATTAATATATTTATTTATTTACTTATGTATTAGTTTGTATATTTTTCATTTTTTTGCGTAAGTACATCCGTCATTTGTAATATTTTTAAATTGTTGTTACCATTTCCAATTATTTTAAATTTAATTTATTGTAATTATTGATATTTAGCGTTTGCTTTTTTTAAATGTTTTTTTAAGCTTTTTTCATATGTAAAAATAAAAGATCTGCACTCATCCAAATTCAGCACAAAATGATTTTTCCATATATTTATAATAATAATAATAATTATAATAATAATAATAATTATTATTATTATTATTATTATTATTTTCTAAGCACTTTAAATTAAATCTTTAAATTGAATCTTTTAAACTAAATAAAAATGAAAAAAAATTGTGTTTGGTGCTTTTATCTTTGCTGGTTGTGGATTAATTTTAAACCATAAAAATCATTTGGTGACATAACCATTGTTCACCTTTTATTACATGTAATGATGCTAACCTGTGACTCTGTGTTCCATCAG
Seq C2 exon
GCCTTTGAAAAACTCAGACAGCTCTCTGATGGATGAACAGCTGAGCGAATGGGCTGAAGACGACACCAATAAACGATTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103554:ENSDART00000158232:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.268 A=NA C2=0.643
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(14.3=12.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGGTGGTCCCCCAAAGACT
R:
CCGGAATCGTTTATTGGTGTCG
Band lengths:
291-1038
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]