GgaINT0038692 @ galGal3
Intron Retention
Gene
ENSGALG00000002922 | NOTCH2
Description
NA
Coordinates
chr8:4233860-4235784:+
Coord C1 exon
chr8:4233860-4233970
Coord A exon
chr8:4233971-4235591
Coord C2 exon
chr8:4235592-4235784
Length
1621 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
GTTGGGTTTGTATTTTTTAGGCC
3' ss Score
8.27
Exon sequences
Seq C1 exon
GAGTGAACTGTGAGAATAACTTTGATGACTGTGCAAGTAACCCATGCGTTCACGGGGACTGCATTGATGGCATTAATCGCTACAACTGTGCTTGCAAACCTGGATTTACAG
Seq A exon
GTAAAGTCAGCTACCTGATAGCTTGAGGTTGTTTTGATGGTAGTTACCCTGTTAGCTAAGGAAGCTGTTCTCTGCATACCGACTGCAAGGGACTCAGTTAATATCTCAGTAGATCCTTCTAATCTTTGCATCTCAGTGTCTTACATTTCAGCAAGTCACACCAAGTGGAGATATGGTCTAATCTGTGCTGTGAGATGCCATTCTTGTTAGGTAATTACATCTAATTCATGGTTCTCGATCTTATAACAAACAAAACCATGTGACTTTGGTTTATTATTCACAGCTTCTTTTCCAGGGGCACAGACTGTGAACAGTGTAGACAGGTGTTGGATTAGACTGTGCCTTGGGCTTGGACTACAACTAGTATTTCTCTTTCAGCAAAAGCAAAGCATGAAGTCAGCGTTCTGTGATGTGATGATGTGATCTGTGCTGTTTCCTCTTCTAAGTTGTGTAAAATCATAAAAACAAGACTGAAAAAAAGCAGCTTTTATGTGCTTCTAAATCCATGCTCAGAACTGTAGGTCTGCATCAGGACTGACTGGTTCTGATGACTAAAGCACATCTCAACTCTGTTTATAATGGACTTAATGCGTTTTGAGGCATGTAGGGTAGCATGCTCATAAAATAATGGTTGTAAGGCAGTTGGTACCATTTGTAGCAGTTTTTTCATCATGTCTGTTTACTGTTTACTACTGAATGATTCTAATTAGAATAGATCTGAAACGCATTAGAAGCAGTGCTAAGAGGTTTCATGTGTTCTTTGTGTTTCTCTTGGCATCTTTTTAAACTTCTAAAGCTTCTTTCTTCCATTGACTCTGTCATGGTGATATTCTTCAGTGCCCATAGCAGGAAGAGGCATGATCCTGATCGTTCTTGCCTTTGGTCCTTCCTCGTTGTTGTCATACCACGTTTGTTATCCTGCTGGATTTCTCACTGTTATCAGTCGAAATAATTCAGAAATGTGATTAATTGACCTGTTCTAGTATTTAAAGAGCCAGTCTGAGTGGGGTTTTGATACCTTGTGCTTTCTATACGTTAAAAACATTTTTCAGCTTCAGGACTCGCTCTGTTTAGCTTTGCAGTCTCACACATTCTTATGGTCAATACTTAAAGGATTTTGCAATTCTGGCACACACTGTAAAGAGAGGAGGCAAAACAGGATACGGTGTTATTTAGAGTTCCTTTTACGCAATAAACCACAAGACCTATATTTACTACAGGCAGTATGGCAGTGTTGGTTGTTCAGAGGGTGGGTAATTTTAGCACAGAAGAGAAGGGCTTTGACAAGTGGAGCTCAAGAGGTTTGTTCCAAATACAACACAGCTGAGTGATTTTTTGCTTTTGCTAAAACGAAACTGAATATTAATTACTGATTTTTCAATGCAGCTCTGTTGAGATTCTTGAGTGGTTTGTAAATACTTGTTGAACATAAGTGTTGTTTTCCAGGTGCAGAAATATTCTGTGTCTTCAGTTAAAGCTACTTAAGCATGAGAGATCTGTACCTCTGCTTCAGCTTTACAGGGTTGTCTCAACCACACCATCTTACAGACTTGCAGGTCAAATGTTCTTGAAAGAAATACGTCTTAATAAGGAATGTTTTGGTTGGGTTTGTATTTTTTAG
Seq C2 exon
GCCCACGTTGTAATGTGGATATTGATGAATGCGCATCCAGCCCCTGTAATAATGGTGGAACATGTATAAATGAAGTCAATGGCTTTCGCTGTGTATGTCCTGAAGGTTACCATCATCCTCACTGCCAGTCACAGGCAGATGGCTGTCTTAGTAATCCCTGTGTACATGGCAACTGCACGCACATTGTTAGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002922:ENSGALT00000039988:12
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=5.3),PF0000822=EGF=PU(90.0=71.1)
A:
NA
C2:
PF0000822=EGF=PD(6.7=3.1),PF0764510=EGF_CA=WD(100=66.2),PF0000822=EGF=PU(53.3=24.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTGAACTGTGAGAATAACTTTGA
R:
CCACTAACAATGTGCGTGCAG
Band lengths:
304-1925
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]