GgaINT0124449 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7832882-7833344:+
Coord C1 exon
chr17:7832882-7833066
Coord A exon
chr17:7833067-7833211
Coord C2 exon
chr17:7833212-7833344
Length
145 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGA
5' ss Score
4.3
3' ss Seq
CTCCTCTCCTCTCCTTACAGTGC
3' ss Score
11.36
Exon sequences
Seq C1 exon
GTATCGACGTCGCTCATCTCTGCAGGAACTCAGGGCTCTGTGTGGACAGTGGCAACACTCACTTCTGCCGCTGCCAGGCTGGCTACACCGGCAGCTACTGCGAGGAGCAGGTGGATGAGTGCTCCCCCAACCCCTGCCAGAACGGAGCCACCTGCACCGACTACCTGGGGGGCTATTCCTGTGAG
Seq A exon
GTGGGAGCTGCTCTCTTGTGTTGGGCTCTTTCTGGGGGTTGCAGTAACTCAGGCGGATCGGGAATAGATCAGTGTTTGTATGTTCTGTGCACCGTGCAGCAGCTGGGTGAAGGTCTCTGACAGCTCTCCTCTCCTCTCCTTACAG
Seq C2 exon
TGCGTGGCTGGTTATCATGGAGTTAACTGCTCAGAGGAGATCAATGAGTGCTTGTCCCACCCATGCCAGAATGGAGGAACCTGCATCGATCTCATCAATACCTACAAATGCTCCTGCCCCAGAGGAACTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:20
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=46.8),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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCGCTCATCTCTGCAGGAAC
R:
GTTCCTCCATTCTGGCATGGG
Band lengths:
257-402
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]