GgaINT0124439 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7828376-7828992:+
Coord C1 exon
chr17:7828376-7828609
Coord A exon
chr17:7828610-7828881
Coord C2 exon
chr17:7828882-7828992
Length
272 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
CCCCCGCTTTCCTCCTCAAGGGC
3' ss Score
9.09
Exon sequences
Seq C1 exon
GTTTCTCAGGTGTTCACTGTGAGATCGACATCGATGAGTGCAACCCCGACCCGTGCCACTATGGGACCTGCAAGGACAGCATCGCCGCCTTCACCTGCCTCTGCCAGCCCGGCTACACGGGCCACCGCTGCGACATCAACATCAATGAGTGCCAGAGCCAGCCCTGCAGAAACGGGGGGACCTGTCAGGACAGGGACAACGCCTACAACTGTCTGTGCCTCAAGGGGACCACGG
Seq A exon
GTAAGCAATGGGAGCACCTGGGGCGGCGGTGCCGGCAAAGCACCCAGCCTATCCTGGGATGGGTTCACCGTGATGCGCTGCTTTAGGGGATGGCCTGGGGAGGGGGTGTCCTCGGCCGGGGCAGGTTTTCCCAGTTTAGCACCCGCACCTCAGCTGGAAGCTGTCTGCGGGGGAGGCTTTGTTGTGGTGCGGAAGCAGCACCCGTGGGGTTTGTTGTGCATCGTCAGCAGGGCCGGGGGCACCCTGCTAACACCCCCGCTTTCCTCCTCAAG
Seq C2 exon
GGCCCAACTGCGAGATCAACCTGGACGACTGCGCCAGCAACCCCTGCGACTACGGCAAGTGCATCGACAAGATCAACGGCTATGAGTGCACCTGTGAGCCGGGGTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:10
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(16.1=6.3),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(93.1=71.1)
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:
TCGACATCGATGAGTGCAACC
R:
GGTGCACTCATAGCCGTTGAT
Band lengths:
302-574
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]