DreINT0105429 @ danRer10
Intron Retention
Gene
ENSDARG00000103554 | notch1a
Description
notch 1a [Source:ZFIN;Acc:ZDB-GENE-990415-173]
Coordinates
chr21:4627117-4627529:-
Coord C1 exon
chr21:4627410-4627529
Coord A exon
chr21:4627270-4627409
Coord C2 exon
chr21:4627117-4627269
Length
140 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
TGTGGTGTGTATGTGTGCAGGTC
3' ss Score
8.1
Exon sequences
Seq C1 exon
GTGAGGTGTGTGAGAATGTTTTAGCCCCTTGTTCTCCACGTCCCTGTAAAAACGGCGGTGTGTGTCGTGAATCTGAGGATTTCCAGAGCTTCTCCTGTAACTGTCCGGCTGGATGGCAAG
Seq A exon
GTAAATGTGTGTGTGCGCTTGCGTGTATTTTAAAGAGAGTGTGTGAGATTCTCAGTGTGTAAAGACAAGAACGTGTGTGTGTGTGTTTGTATTTGTCTCTTCATCATAATAATCTCTTCATGTGGTGTGTATGTGTGCAG
Seq C2 exon
GTCAAACGTGTGAGGTGGACATTAATGAGTGTGTGAGGAACCCGTGCACTAATGGAGGAGTGTGTGAAAACCTGCGCGGTGGATTTCAGTGCCGCTGCAATCCTGGATTCACTGGAGCTCTATGTGAAAACGACATTGACGACTGCGAGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103554:ENSDART00000158232:2
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(6.5=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0764510=EGF_CA=WD(100=73.1),PF0000822=EGF=PU(9.7=5.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAGCCCCTTGTTCTCCACGT
R:
TCGCAGTCGTCAATGTCGTTT
Band lengths:
248-388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]