GgaINT0124450 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7833212-7833914:+
Coord C1 exon
chr17:7833212-7833344
Coord A exon
chr17:7833345-7833656
Coord C2 exon
chr17:7833657-7833914
Length
312 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
TTGTTCCCCCATTTCTCTAGGGG
3' ss Score
9.42
Exon sequences
Seq C1 exon
TGCGTGGCTGGTTATCATGGAGTTAACTGCTCAGAGGAGATCAATGAGTGCTTGTCCCACCCATGCCAGAATGGAGGAACCTGCATCGATCTCATCAATACCTACAAATGCTCCTGCCCCAGAGGAACTCAAG
Seq A exon
GTAAATTAATTCCCCAGGCTGGGGCATTAGCGGGTGGAATGCAGATATCCTTGGTATCTGCTCATTAGCTGCTCGGGCTTGCAGAAGCAAATGCAGCAATAGAGGATTGCGTGTGCTGGCGGGCTCAGCCATCAAGGCCACGTGGCCTTGGGCACGAGCTGCATGGGCTGCGTGCTTCCCACTGAGCGGTGGCTCAGACTGCCATTGAGTTGGTCAGGCTCAGCCCCTTCGCAGGGAAGGTTCGCACGAGGGACCTCCGAGCCCCCCGATACTGTTTGATGAGCTGTGTGGGTTGTTCCCCCATTTCTCTAG
Seq C2 exon
GGGTGCACTGTGAGATCAATGTGGATGACTGCAGCCCTTTCTTTGATCCCGTCACCCTGGGGCCCAAGTGCTTTAACAATGGCAAGTGCACGGATCGGGTAGGTGGCTACAGCTGCATCTGCCCCCCTGGCTTTGTAGGGGAGCGCTGCGAGGGAGACGTCAACGAGTGCCTCTCCAACCCCTGCGACGCGCGCGGCACCCAGAACTGCGTGCAGCGGGTCAATGACTACAAATGCGAGTGCCGGCCTGGCTACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:21
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),PF0000822=EGF=PU(90.9=34.5)
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:
GCTCAGAGGAGATCAATGAGTGC
R:
CGGCACTCGCATTTGTAGTCA
Band lengths:
349-661
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]