RnoINT0102206 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3923819-3924603:-
Coord C1 exon
chr3:3924411-3924603
Coord A exon
chr3:3923965-3924410
Coord C2 exon
chr3:3923819-3923964
Length
446 bp
Sequences
Splice sites
5' ss Seq
TGGGTATGG
5' ss Score
6.23
3' ss Seq
AAACAGAGGCCTCTCTACAGATA
3' ss Score
0.72
Exon sequences
Seq C1 exon
GGAGCATGTGTAATGTCAACATTGACGAATGTGCGGGCAGCCCCTGCCACAACGGGGGCACCTGTGAGGATGGCATCGCCGGCTTCACTTGCCGCTGCCCCGAGGGCTACCACGACCCTACGTGCCTGTCTGAGGTCAACGAGTGCAACAGTAACCCCTGCATCCATGGAGCTTGCCGGGATGGCCTCAATGG
Seq A exon
GTATGGCAGACTGGCCTGGGGGGAACCAGCTAGAAGCCTGGGGCAGATACGGACTGGGTGAATGGGTGTTCCTGTGAGACCAGTAGTGTGAGGTCAGCCCCAAGAGTCTTCCCAGCATCCCTGGGTTGTGTCCTTATTGGCTAACATCAGCTCAGGATATAGACCTTAAGCACCCTGGCTGTTGAAACGGTCGTCTGATACCTGTGACAGCAGCCCTCTGTCAGTGTGTATATGGGGAGACTGCTAAAGTCCTTATTCAAACTGTTAAAAAGTTTGGTACAGAGGGTCAGTACTGGGTCACACTGTCCCAGTCTAGAACCCTTGCATGGTCTTGGGAAAGGCGGGTACCTCCAGTCCAGTAGATGATGTGTCCTTGCCCTCAGACTGGATCTGTAGTCTAGGAACTGTATCTGTAGCCCAGGCTACAAACAGAGGCCTCTCTACAG
Seq C2 exon
ATACAAATGTGACTGTGCCCCTGGGTGGAGTGGGACAAACTGTGACATCAACAACAATGAGTGTGAGTCCAACCCTTGTGTCAACGGTGGCACCTGCAAAGACATGACCAGTGGCTACGTATGCACCTGCCGAGAAGGCTTCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:13
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(3.4=1.5),PF0000822=EGF=WD(100=58.5),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:
GGAGCATGTGTAATGTCAACATTGA
R:
TTCTCGGCAGGTGCATACGTA
Band lengths:
329-775
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]