GgaINT0124444 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7831232-7831605:+
Coord C1 exon
chr17:7831232-7831351
Coord A exon
chr17:7831352-7831452
Coord C2 exon
chr17:7831453-7831605
Length
101 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCCATCCCGCTGTCCCGCAGGCC
3' ss Score
10.11
Exon sequences
Seq C1 exon
GAGCCACCTGTGAGGACGTGCTGGCCCCCTGCGCCGGCGGCCCCTGCAAGAACGGCGGCGAGTGCCGGGAGTCAGAGGACTACAAGAGGTTCTCGTGCAGCTGCCCGCCCGGCTGGCAAG
Seq A exon
GTGAGCCTGCTCTGCGGGGTGGGCTTGGGGCGCAGTGACCAGCCCTGGTGCTTCTGCCAGTGCCCCCCGGCTCATGTGGTTCCCATCCCGCTGTCCCGCAG
Seq C2 exon
GCCAGACGTGTGAGATTGACATCAATGAGTGTGTGAAGAGCCCGTGCCGCAATGGGGCCACGTGTCAGAACACCAACGGGAGCTACCGCTGCCTGTGCCGGGTGGGCTTCGCGGGCCGCAACTGCGACACCGACATCGACGACTGCCAGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:15
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(6.5=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0764510=EGF_CA=WD(100=73.1),PF0000822=EGF=PU(9.7=5.8)
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:
CACCTGTGAGGACGTGCTG
R:
CGATGTCGGTGTCGCAGTTG
Band lengths:
254-355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]