GgaINT0124441 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7829672-7830096:+
Coord C1 exon
chr17:7829672-7829864
Coord A exon
chr17:7829865-7829950
Coord C2 exon
chr17:7829951-7830096
Length
86 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
GCTCTTGTTTTTCCCCAAAGTTA
3' ss Score
6.54
Exon sequences
Seq C1 exon
GGCGCATGTGCAACATCAACATCGATGAGTGTGCCAGCAACCCATGCCACAATGGGGGCACATGCAAGGATGGCATCAACGGCTTCACCTGCCTCTGCCCCGAAGGCTTCCATGACCCCAAGTGCCTGTCCGAAGTGAATGAGTGCAACAGCAACCCCTGCATCCACGGGAGGTGCCACGACGGGCTGAACGG
Seq A exon
GTAGGCTGGGGCACAGCACTGCTCACACCAAAGCACGGTCAGGTGGCACCAAAACCTCTGCTTTATGCTCTTGTTTTTCCCCAAAG
Seq C2 exon
TTACCGCTGTGATTGCGACCCGGGCTGGAGCGGGACAAACTGTGACATCAACAACAACGAGTGTGAATCCAACCCCTGCATGAATGGTGGCACCTGCAAGGACATGACCAGCGGTTACATCTGCACCTGCAGGGAGGGGTTCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:12
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(3.4=1.5),PF0000822=EGF=WD(100=47.7),PF0000822=EGF=PU(53.3=24.6)
A:
NA
C2:
PF0000822=EGF=PD(43.3=26.0),PF0000822=EGF=PU(90.3=56.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGGCTTCCATGACCCCAAG
R:
CAGGGGTTGGATTCACACTCG
Band lengths:
170-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]