GgaINT0124431 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7821657-7822728:+
Coord C1 exon
chr17:7821657-7821919
Coord A exon
chr17:7821920-7822389
Coord C2 exon
chr17:7822390-7822728
Length
470 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTCCTTCCCTCCCTCCCCAGGTA
3' ss Score
13.55
Exon sequences
Seq C1 exon
GTGCAGCAGTGCCCATATGGGCGAGCGGTGCCAGCTGCCCAACCCCTGCCTCAGCTCCCCCTGCAAGAACGCCGGCACCTGCATCCCCCTGCTGCGTGGCAGCACCGCCGACTACACCTGTGTCTGCCGCCTGGGCTTCACCGACGAGCTGTGCCTCACACCCCTGGACAACGCCTGCCTCAACAACCCCTGCCGCAACGGGGGCACCTGTGACCTGGTGACACTCAGCGAGTACAAGTGCCGCTGCCCGCCGGGCTGGTCAG
Seq A exon
GTGAGGGGTGGCCCTCCCACGGTGGGACAGGATGGGATGGGGTGGGGTGGGACAAGAGTTGTGCTAGGAGAGGTTCAGGTTGGATGTTAGGACACGGTGGACTCGGTGTCCCTGGAAGTGCTCCAGAACAGGGGAGATGTGGCGCTGGGGAACATGGTTAGTGGGATGGGTTGGGCTTGGGGATCTGAGAGGGCTTTTCCAAACTGAATGACTCTGTGATTTGATGGGATGGGATGAGCAGCCTTTGCTGAGGGCTGCTCCTTGAAAGCCCCACTGCTGGAGAAGGGCACTGAGGTTTTTCTCTGTCGGCACTGAAGACAAATGGAGAGGGTTGGCATAGCTGAGCTTGGGAAACGCTCAGCTGGGGGAGTTATTTGCACCCCCCTGTGAACACAGCTCTTGTGTTGGCTCCGTACCCCAGCACTAAGAGCTGCTCTTTGCATCCTCCTCTTCCTTCCCTCCCTCCCCAG
Seq C2 exon
GTAAAACCTGCCAGCAGGCCGACCCCTGTGCCTCCAACCCCTGTGCCAACGGGGGTCAGTGCGTCCCCTTCGAAGCCCACTACATCTGCCGCTGCACGGCCGGCTTCCACGGGGCCAACTGCAAGCAGGACGTGAACGAATGCAACATCTCACCACCAGTCTGCAAGAACGGTGGCAGCTGCACCAACGAGGTGGGCACCTACCAGTGCTCCTGCAAGCCAGCCTACACCGGGCAGAACTGCGAGCATCTCTATGTGCCCTGCAACCCCTCGCCCTGCCAGAATGGGGGCACGTGCCGCCAAACTGGGGACACCACCTACGACTGCACCTGTCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:2
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=WD(100=40.4),PF0000822=EGF=PU(90.6=32.6)
A:
NA
C2:
PF0000822=EGF=PD(6.2=1.8),PF0000822=EGF=WD(100=27.2),PF0764510=EGF_CA=WD(100=36.0),PF0000822=EGF=PU(81.2=22.8)
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:
GACAACGCCTGCCTCAACAA
R:
GGCACATAGAGATGCTCGCAG
Band lengths:
356-826
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]