GgaINT0038693 @ galGal4
Intron Retention
Gene
ENSGALG00000002922 | NOTCH2
Description
neurogenic locus notch homolog protein 2 precursor [Source:RefSeq peptide;Acc:NP_001238962]
Coordinates
chr8:4194710-4196689:+
Coord C1 exon
chr8:4194710-4194902
Coord A exon
chr8:4194903-4196543
Coord C2 exon
chr8:4196544-4196689
Length
1641 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TGTTGCTTTTGCCTTTGAAGGTA
3' ss Score
10.23
Exon sequences
Seq C1 exon
GCCCACGTTGTAATGTGGATATTGATGAATGCGCATCCAGCCCCTGTAATAATGGTGGAACATGTATAAATGAAGTCAATGGCTTTCGCTGTGTATGTCCTGAAGGTTACCATCATCCTCACTGCCAGTCACAGGCAGATGGCTGTCTTAGTAATCCCTGTGTACATGGCAACTGCACGCACATTGTTAGTGG
Seq A exon
GTAAGTCCTTCCTGGAACACCAAATGTATCTACTGCCTTTTATACTTTCTTCCCCACCTCCACCACCCTGAGTTCCACCTTGATTAGAGGTTTCTGAATTTTAATTTCTCAGATTACTTGTTTGCTGGCCATGAAGTAATCACAGTAAGGTGTAGACCTTTATTCTCCAGCTGCCCTTTGTGCTGTTTCAGGGTGAGTTTGTCTGCCCTGCATGGGCACCATCGAAAGGGGAGAGTTCAGTAGTTCAATCTAATAGAGTGAATGCAATTAAAATAAAGAAGTGGTTCCAAGCAAAACTGTTGGAAAACAGCAGATGCTTTATCAAAGTCTAAAGTGTTGAGTGTGGACAGTGTGTTGGTGACTAAAGCCATTATTGCTAACCAAATAGTAACCTTCTGCATGAAGGAACAAGCAGGTAACTCGGAAAACTAGGAGGCAGAGTAGTTTTGGAAGATCAGGTGGGGAAATTTTGGTGTAGCAACCAATCACAGGTGGTACTTCAAGGCTTGGAAAAGGAGCTCGGGATGAAAAGTCAAGGAGAAGGTAAAAATGAGATGTTGATGCCCTCCATCTCAGTCATCTGCTTTTAGGGGAAAAGTTGGTGGTTGGTGTTTTGTTTGTTTGGTCTAAGCAAGGCATCCTGTTTAAGTTGGTACATTGATGGAATGCAGTTGCCTCTGACTGTTTCCTCTAGCAGCTTTCTCAAGATTAGGAGATTTATTGTTGAGCAGTGGTTGTCTTAAGAACAGCATAGCCAAGGCAGATTTAATCGGCTTTAGTCACACTGTTGCATGCCTGTGAGAAGAAAAGAAAGCTTTTTCTGGCCGTTCTGATGGCACCAGTTGTTGCTGAATCATCCCATCCAGGAAGACCAAATGCTGACTTCGTGAGCCTTGAATCAAGACCTCTTTTTGTTAGGGATGAATCCGTGGTGAATGAATTACACGGGCTCTGGGAGCACAGGGGCTGTGGAGCTGACAAGCGGAGGCAGGGACAGGGTCATAGCTGTGAAACTTCCCTTGGTCCAGAGTAGTAGTGGCTTGCATGCATGTTGTGTCCTGGAAAGTGTTGTCAGCACTTGGCAAGGAAGGGTTTTGCCACAGCTGTAGGGCAGGATTCAGCGCTTTTCTGGAGCTGACAGGAAGGCTGCCTTTATGTCAGGTTCAGCCTTCTTGTTTATGCCCATGTGTACCTTATACTTGGTGTGAGATAAAATTAGTGTTGTCTGCATGATGGAGAAGGAGGCCAGCATGCATTTTGTGTGGCTGGAGTCCAGGGTGATTCAGTAAGACTTTGGTTCTATGTCATGTGGGTGGAGAGCTGCTCCACTTCAGATTCTGAAACATGGTAGAGTAAATTGCTGCTGCTCCCAACCACCTGTTTTCACTGGTAACCACTACTTTGTATTAAATTAGTCCACTCATCTTTGGCACCTACTGTTCCTCTCTGCTTTCTGTCATGTTTTCTCCCTGCCTTTATTTAAATGTATTGAGATGGTCTTGTCAAAACAGAAACGTATTGCTGTCTTAGAGCTTCACGGAGGCTGTTAACAGGAGGGAAGTGTGTTTGTAAGGGTGGTTTATTTTCAGTATTCTGTCATTTCAAAATGTTCTCCAATTCCTGTTGCTTTTGCCTTTGAAG
Seq C2 exon
GTACAAATGTGTCTGTGACCCAGGCTGGATAGGAGATTACTGTTCAACAGAAGGGAACGAATGTAAATCAAACCCGTGCCAAAACGGAGGGACTTGTGAGGATCTGCTGAATGGATATAGGTGTACCTGCAGGAAAGGATTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002922:ENSGALT00000039988:13
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(6.7=3.1),PF0764510=EGF_CA=WD(100=66.2),PF0000822=EGF=PU(53.3=24.6)
A:
NA
C2:
PF0000822=EGF=PD(43.3=26.0),PF0000822=EGF=PU(90.3=56.0)
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:
CACGTTGTAATGTGGATATTGATGA
R:
TTGAATCCTTTCCTGCAGGTACAC
Band lengths:
334-1975
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]