DreINT0105435 @ danRer10
Intron Retention
Gene
ENSDARG00000103554 | notch1a
Description
notch 1a [Source:ZFIN;Acc:ZDB-GENE-990415-173]
Coordinates
chr21:4621771-4623337:-
Coord C1 exon
chr21:4623205-4623337
Coord A exon
chr21:4622029-4623204
Coord C2 exon
chr21:4621771-4622028
Length
1176 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
TTCTCCGCTCATGTTTTCAGGAG
3' ss Score
8.8
Exon sequences
Seq C1 exon
TGCGTTCCTGGATATCATGGTATGAACTGCAGCAAGGAGATAAACGAGTGTCTTTCTCAGCCCTGCCAAAATGGAGGAACCTGCATCGACCTCGTGAACACCTACAAATGCTCCTGCCCACGAGGAACACAAG
Seq A exon
GTACATACACTCGCATACAACAGATTCATCATACAATACTTCCCTCTGCAGTGCTTTGACTCTTTTCTATTTGCTCTTGTTTGGATTCTTTTCTCTGCTTCTATTCTGATTCTTTTCTCTTTGTTTCTGTTTTGATTCTTTTAGCATTGTTTGTTCTGATTCTTTTTCTCTGCTCCTTTTTTGATTCTTTTCTATTTGCTCTTGTTTTGATTCTTTTCTCTGCTTCTATTCTGATTCTATTCACTTTGCTTCTGTTTTGATTCTTTTAGCATTGCTTGTTCTGATTCTTTTCTCTTTGTTTCTGTTTTGATTCTTTTAGCATTGCTTGTTCTGATTCTTTTCTCTTTGTTTCTGTTTTGATTCTTTTAGCATTGTTTGTTCTGATTATTTTTCTCTGCTCTTTTTTTGATTCATTTTCTATGCATATGTTTTGATTCTTTTCTGTCTGCTCCAGTTTTCATTCTTTTCTCTTTGCTCCTGTTTTGATTCTTTTAGCATTGCTTGTTCTGATTTCTTTTACCTCTGCTCCTGTTTTGATCATTTTCTCTGCTCCTAATTTGATTATTTTCTCTGCTTCTGTTCTGCTTCTGTTCTCTTTGCTCCTGTTTTGATTCTTTTAGCATTGCTTGTTCTGATTCTTTTTATTTGCTCCCGTTTTGATTTCTTCTAGCTCCTTTTTTGAATCATTTTCTGTGCTCTTGTTTTGATTCTTTATCTTTGCTCCTGTTTTGATTCTTCTTCTCTGATCCTGTTTTGATTCATTTCTCTGCTTCAATTCTGATTCATTTCTCTTTGCTTCTGTTTTGATTCTTTTAGCATTGCTTGTTCTTATTCTTTTTCTCTGCTCCTTTTTTTTAATTCATTTCTATGCATATGTTTTGATTCTTTTCTCTTTGCTCCAGTTTAGATTCTTTTCTGTCTGCTCCTGTCTTGATTCTTTTAGCATTGCTTGTTTTGATTCCTTTTCTCTGCTCCTGTTTTGAATCTTTTCCCTTTGCTCCTGTTTTGATTCCTTTTCTCTGCTCGTATTTTGATTATTTTTGTTTTGTTTGCGTTTTGACTCTTTTTTTTGACTCTTGATTATCTTAACTTTGCTTGTGTTTTGACTCCTTTGCTTTGCTCCTGTTTTGATTCTCTGCTCGTGTTTTGACTCTTTTTCTCCGCTCATGTTTTCAG
Seq C2 exon
GAGTTCACTGTGAGATTGATATTGATGACTGTTCTCCATCTGTGGATCCGTTAACCGGAGAGCCGCGGTGTTTTAACGGCGGGCGGTGTGTGGATCGTGTCGGTGGTTACGGTTGTGTGTGTCCGGCTGGTTTTGTGGGCGAGCGTTGCGAGGGTGACGTTAACGAGTGCCTGTCAGACCCCTGTGACCCCAGCGGATCCTACAACTGTGTTCAGCTCATCAACGACTTCCGCTGCGAGTGCCGTACAGGATACACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103554:ENSDART00000158232:8
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(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
A:
NA
C2:
PF0000822=EGF=PD(6.5=2.3),PF0000822=EGF=WD(100=44.8),PF126612=hEGF=PU(69.2=10.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTGTCTTTCTCAGCCCTGC
R:
GTGTATCCTGTACGGCACTCG
Band lengths:
344-1520
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]