RnoINT0102221 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3912954-3914288:-
Coord C1 exon
chr3:3914140-3914288
Coord A exon
chr3:3913171-3914139
Coord C2 exon
chr3:3912954-3913170
Length
969 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CCTGCCGCCCCTGCCCGCAGGTG
3' ss Score
12.99
Exon sequences
Seq C1 exon
CTCCATCGTCTACCTGGAGATCGACAACCGGCAGTGTGTACAGTCATCCTCGCAATGCTTCCAGAGCGCCACCGATGTGGCTGCCTTCCTAGGTGCTCTTGCCTCCCTCGGCAGCCTCAATATCCCCTACAAGATCGAAGCCGTAAAGA
Seq A exon
GTGAGTGACCAAGGGCTGGAGGGGCGGCTCAGTGGTTAAGAGCACGGGCTGCTGTTGCAGAGGAGCTGGGTTCAAGTCCCAGCACCCATGCAGCATCTTAATAACTCTCTGTAACGCCAGTTCCAGAGCGCCCAGGACCTTCTGACCTCTGAAGGCACCAAGCGTGCACAGGGTCCTGACATACATGCAGGCCAAACACCCATGCACATTAATTTTTTTTTTTAAATAAGTGCCCTACCCCTGCCAGCCCTGCCTCTTCGGGGATGGGTTCCTTGCGTGGAGGAAAGTCTGAGAGGGTCACAAGCAGGCCATCTCTTCACTCCTTGTGCCCAGTTGTCATCCCCAGCTCAGGAAGTGCTTTTCTGGAATATTTTCCATGGCCTTTCCCCGCTGTGGATGGTGGGAACTATAAGTACAAACTGCCCCCTAAGATGAATACATGTACCAGAAAGTGTGGAGGAGCCTTTCCTCTCTCCCCATTTTCTACCCCTGATTTTTCTTTGTTGGATATTATTTCAAAATCATTACTGGGGTTTTGTGTGTGTGTGCGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGTTTTTTTTTTTTTAAAGAGAGAGAGAAGAATTGATCGGTGTCATGTGAAGTGTTGAAGTTTGTATCTTGAAAATCCCCCTAAATCCTTTGTCTTAACAGCTCAATGCGAGCGCAGTGATTTGAAGTTCGCTAATCCTCCTTCTCGAAAGGGGAGAAGTGAGCACTGTCTCCAGACAGATCAGCCGGTGCAGAAGAGAATTTAGCGATAGTTTGCAATTCTGATTAATCACGTAGAAAATGACCTTATTTTGGGGGGTGGGATGGAGGAGAGTGGGTGAGGAGGCACTGGCCGTGGAGCCAGTCCGCCGCCCCCCACCAGCCCACAGCATCGCCACGCCTGACGTGGGGTGCTTGCCTGCCGCCCCTGCCCGCAG
Seq C2 exon
GTGAGACGGTGGAGCCTCCGCTGCCCTCACAGCTGCACCTCATGTACGTGGCGGCAGCTGCCTTCGTGCTCCTGTTCTTTGTGGGCTGTGGGGTGCTGCTGTCCCGCAAGCGCAGGCGGCAGCATGGCCAGCTCTGGTTCCCTGAGGGTTTCAAAGTGTCAGAGGCCAGCAAGAAGAAGCGGAGAGAACCCCTCGGCGAGGACTCAGTCGGCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:27
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=0.233
Domain overlap (PFAM):
C1:
PF076847=NODP=FE(79.4=100)
A:
NA
C2:
PF076847=NODP=PD(14.3=12.3)
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:
TACCTGGAGATCGACAACCGG
R:
TTGAGGCCGACTGAGTCCTC
Band lengths:
356-1325
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]