RnoINT0102242 @ rn6
Intron Retention
Gene
ENSRNOG00000018835 | Notch2
Description
notch 2 [Source:RGD Symbol;Acc:3188]
Coordinates
chr2:200286921-200287561:+
Coord C1 exon
chr2:200286921-200287040
Coord A exon
chr2:200287041-200287408
Coord C2 exon
chr2:200287409-200287561
Length
368 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACG
5' ss Score
10.19
3' ss Seq
TCCTTACCCTTTCTTTATAGGTC
3' ss Score
11.4
Exon sequences
Seq C1 exon
GCAAGAATTGTCAAACGGTGTTGGCGCCCTGCTCCCCTAACCCGTGTGAGAACGCTGCAGTTTGTAAAGAGGCACCCAACTTTGAGAGCTTCACCTGCCTGTGTGCCCCTGGCTGGCAAG
Seq A exon
GTAACGATCCCGGATGCATGCTGCACCGTAAACAAAGATGACATGGGAGGCCACAGGCTCTTTGGACAGGAGCCACTAGCTGGAAGGGCTCCTAAGACCTTCCCAGATTTCATCTGTATAGTCCTCAAGTAGCTGAGACCCTCCAACCCAAGAGTTTCAAGCTATGAGTAGCAGTTGGGAGGAGTTTCTCAGGGACATAAATGCCTTACTGGGACCTCCTGCATCGGACCAATCAGGTGGCCTTCTGCATCAAAACACTCTAAGCTCATGGTGTACTAAAACTTACACCTACCCAGACTTACACCCTGCCTTGATCTCTGTGGGAATTTTCTTCTGAAGCCTGGCTATTCCTTACCCTTTCTTTATAG
Seq C2 exon
GTCAGCGCTGTACAGTTGACGTTGATGAGTGTGTCTCCAAGCCGTGTATGAACAATGGCATCTGCCATAATACTCAGGGCAGCTACATGTGCGAGTGCCCTCCCGGCTTCAGTGGTATGGACTGTGAGGAGGACATCAATGACTGCCTTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018835:ENSRNOT00000025718:16
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=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0000822=EGF=WD(100=57.7),PF0000822=EGF=PU(9.7=5.8)
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:
AGAATTGTCAAACGGTGTTGGC
R:
TGGCAAGGCAGTCATTGATGT
Band lengths:
270-638
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]