GgaINT0124452 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7834006-7835103:+
Coord C1 exon
chr17:7834006-7834118
Coord A exon
chr17:7834119-7834531
Coord C2 exon
chr17:7834532-7835103
Length
413 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
CCGTGCTGTCCCCTCCCCAGGGC
3' ss Score
10.71
Exon sequences
Seq C1 exon
GGCGTCGCTGTGACACCGTGGTGGATGGCTGCAAGGGCAAACCCTGCAGGAATGGGGGAACGTGCGCTGTGGCCAGCAACACCGGCCGCGGCTTCATCTGCAAGTGCCCCCCG
Seq A exon
GTAGGTTCCCGCTGTGCTCCTGCTTTGAGCGTGGGGAAATGAGCCCCTTCCATTGGGAGGAGAATCCACGCATCCAAGCCTTCTTCATCTGCTGGGTCAGGGAGGAGCAGGAGAGTCAGCGCTGCCGGTGTGACACCCAGCTCTGGGGCAGGCTCCTTTCTGCCTGGTGGGGGACGGTTCATGCCACGTAAATGTGGGACAGGCAGAGATGGAGAAGAGTTCCCTTTGTTTTCAGGGGGATGCTCTAATGGGGTTCGTGCTGTAGGTGATTTTGCCCATCACTAGTTTCAGAGGCGGCACCACAGCTGTGCCCTTAGATCTGATTCACCACGTTTGGGCTGAGTTTCCCAGCGCACACACGTGCGGTCCTACCAGGCCATAGGACTGACCCCTCCGTGCTGTCCCCTCCCCAG
Seq C2 exon
GGCTTTGTGGGTGCCACCTGCGAGAACGACTCCCACACCTGCGGGACCCTGCACTGCCTGAACGGTGGCACCTGCATCTCCATGCACAAGAGCTCCAAGTGTGTGTGCGCAGCGGCCTTCACGGGCCCCGAGTGCCAATACCCGGCCAGCAGCCCCTGCATCTCCAACCCCTGCTACAACGGGGGCACCTGCGAGTTCCTCAGCGACGCCTCCCCTTACTACCACTGCAACTGCCCCGCCAACTTCAACGGCCTCAACTGCCACATCCTCGACTTTGATTTCCAAGGCGGCTTCGGGCAGGACATCATCCCACCCAAAATCGAGGAGAAGTGTGAGATCGCCGTTTGTGCGAGCTATGCTGGCAATAAGATCTGTGATGGGAAGTGCAACAACCACGCCTGCGGCTGGGACGGCGGCGACTGCTCGCTCAATTTCAACGACCCCTGGAAGAACTGCTCACAGTCACTGCAGTGCTGGAAGTACTTCAATGATGGCAAGTGTGACTCGCAGTGCAACAACGCGGGCTGCCTGTATGATGGGTTTGACTGCCAGAAGTACGAGGGGCAGTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:23
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(6.1=5.3),PF0000822=EGF=PU(79.4=71.1)
A:
NA
C2:
PF0000822=EGF=PD(14.7=2.6),PF0000822=EGF=WD(100=17.8),PF0006612=Notch=WD(100=19.4),PF0006612=Notch=WD(100=19.9),PF0006612=Notch=PU(15.0=3.1)
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:
CAAACCCTGCAGGAATGGGG
R:
GTCGAGGATGTGGCAGTTGAG
Band lengths:
349-762
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]