RnoINT0102239 @ rn6
Intron Retention
Gene
ENSRNOG00000018835 | Notch2
Description
notch 2 [Source:RGD Symbol;Acc:3188]
Coordinates
chr2:200281746-200283365:+
Coord C1 exon
chr2:200281746-200281938
Coord A exon
chr2:200281939-200283219
Coord C2 exon
chr2:200283220-200283365
Length
1281 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
ACACCTCTGTCTTCTTGCAGCTA
3' ss Score
11.62
Exon sequences
Seq C1 exon
GGCAGAGGTGCAACATAGACATTGATGAGTGTGCCTCCAACCCCTGTCGCAAGGGTGCGACGTGCATCAATGACGTGAATGGTTTCCGGTGTATGTGCCCTGAGGGACCACACCATCCCAGCTGCTACTCACAGGTGAACGAGTGTTTGAGCAGTCCCTGCATCCATGGAAACTGTACTGGAGGTCTCAGTGG
Seq A exon
GTGAGTAGCTGCCATTGCTCACAGCTTCCAACGGGCCTGCATGTGCTAGCTAGAAGCTACTAATTGGCCTCGGTCAAAGCCAACTGAAGGAAACACTAACACAATAGCTCGTATCTGTCAGTTGGGAACTTGACCTGATATTTAGGTTGTCCAAATCACTGCTTTGTCTGTAGAACCTGACCCATCTTCTCAGGCTGAGAACTTACTTGAGAAATAAGGACTGTTTCCTTTACATAAGTAATCAATGAGGACCCCACGGAGGGCCCAGGAATCCGTGCATCTACAATTGTGTTTATATTACAGGATTGAGATCTGAGGGCACAGATTGACAACCCCACACCTTACAGCCTATCCCTGTTCAGTTGTGGAGCCTGCGGTAGTCCATTTGCTGCCTGCATGCCCTCAGAGCTGTTTGGCATGCGATGGCTTTAGAACAAGAGTGTCTTAGACACGATGAGCGGCTGTATGCTCTTGTCATAACACAGCGTGGGCATTGCCACGTCTCAAACTCAAAGAAAGGAGAACATGTTAGATAAGTTTGTTTCCAATCCAGAACATGATGATCTTCAAGACACCCCACCATGGCTCTCTCTCCTCCACTCTTTCTCTCCATTCTCCTCCCACTTCCCAGCTCCCCTTCTCTGACTGATCTGATACAACATGTAACTACTAGCGATGTTGGGGTCAGATGTTATATGTGTTTCGGGTATCTTCAGCTTGTCTTGCTCGATACCACGCTCTCTGAGGCAGGATCTTGATCCTAAGAAAGCGAGCCTGACCTGTAAGACTCTAGTCAACCTCAGCAGGCTTCAGTGGCTTATTTTCTGATGTTTGTACTAGAGGTTCTGAGCTTTGTTCGTGTTCATGTTTCCTTTGATTGCCCCAGTATGTTTGACAAATCATAGCTCTGTGGCAGTCCACCAGCTTCCGGTGAGCCAGTTGGAAGCATATGCTGGTCTTCCAACTGAACATGCTAGATGGATTCATGTCCTTACCATGTGACGGTGATTCCAGTACAGATCCACAGAAACGCAGAAATGAGCTCACGCCTGTAATCTTTGTACTAGGGAGGCTTAATCAGGAAGATTACCATGAGTTCGAGGTGAACCTAGACCACATAGTGAGTTCTAGGACAGCCTGGGCAACAGAGTGAGACCCTGTCCCCAAAATACCAGACAAAAGAAAAGGAAGGATGCACCTGTCTTCCACCTATCTCTTATGTGCCTCTTAAGACTCAGTTGTACCTTTGTACCACACAGTAACACCTCTGTCTTCTTGCAG
Seq C2 exon
CTATAAGTGCCTCTGCGATGCAGGCTGGGTTGGTATCAACTGCGAAGTGGACAAAAATGAGTGTCTTTCTAACCCGTGCCAGAATGGAGGGACATGTAATAACCTGGTGAATGGCTACAGGTGTACATGCAAGAAGGGGTTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018835:ENSRNOT00000025718:13
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=55.4),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
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGGTGCAACATAGACATTGA
R:
TGAACCCCTTCTTGCATGTACAC
Band lengths:
334-1615
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]