RnoINT0102202 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3949145-3951025:-
Coord C1 exon
chr3:3950729-3951025
Coord A exon
chr3:3949224-3950728
Coord C2 exon
chr3:3949145-3949223
Length
1505 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
CTCTTCTGACCCTTTCCCAGGCT
3' ss Score
7.63
Exon sequences
Seq C1 exon
GGGAGGGAGCGCAGGGGCGTGGGGCGCAGGGCGCGGGTGCGAGCGCAGTGAAGGAACGAGCCTGGGTGCCTGTAGTGCCGGGGAGACCCTGAGAGCCCAGCGCCGCCCACCCGCCAGGAAAGAGGGCAGCAGCGGGTGGACGCCCGCGGGACCGCCCGTGGTGCGCGTGAACGTCCGATCCCCGCCGGCCACCGCAAGAGGCCGCCGCCCCGGCAGCGGGCAGCTGGCGAGCAGGCATGCCGCGGCTCCTGGCGCCCTTGCTCTGCCTAACGCTGCTGCCCGCGCTCGCCGCAAGAG
Seq A exon
GTAGGCGCCCGCGAGCCCGCAACTTCGGGCGCCCTTCGGAAACTTCTGGTGCGCCCTGCGCACTCTCTGGGTAGATAGGATTAAGGGACCAGATGCCAGAGCGGGTGGACGGGACATGGAACCTGATGTCCTGGTGTATGAGAGGGACTCCTCCTTCCAGGGGTACCGATTTTTCTCATAGCGCCCAAAGACGCTGAAAGTTTGGTATGGGGCTCTGGGGCTTCGAGGCCGGGTGGCCCGGGAGGCCCAGCCCTGGCTCGCACTTGGGCAGACACTCCTGGGGCTCGCCTCGGGGGCGGACATGCTGCTTGCGCCTGCTACTTTTCGATTTGAATCGAATCGGTTTTGGTTTCCTGTTGCTTCTTGGGACCATTTATTTTCTTTCTTTTTTGCCTCCGGCCCGTGCTGGGGCGGATGTTGGGGTGCAGTATGAGGTCAGGGGCGCTATGCTCGCGTTGCTTACTTAGAGCAGGGCGGAGACGATGTGCCCTGACTTCTAGTATGGGGTTTCAGGATCACTGTCCCCTAGCCGGAATCAAACTTTAGAAGAGGGGCGATGTGCAAGCGGCAGCCTAGGGTGGGGGTGGGACTGACTCACTTTGGAAGTTTGGAAATCCTGCGCCGATTGGAACGGGGGTGGGGGGGGGCGCTTATTTCCCTGCCGGCTCCAGGAACTGGGGACTCCTGTCGTAGTAACCAACTGCACTCTTCTCCCAGTAGTTGGAGAGAACTGCCTACCCTTTCCTTAAAAGTGGGGTTTTATGTGATGCTCCAGTTTGGCCCCCACTTCGGGGCTTAATTTCTTAAGATGGGGTGGGAGGGGCTTGATTAATAGCCCCTTCCCGAGAATAGGGTGGAATTCCTTCTAAGTGAGGTTTCTAAGACCCCCTCCCTGGGTGCGGCGGGGGCTGCCCCTGGAGATGCCTGCGAACAGGTATTGGGTGTCGGAGGAGGCGGGGCAGGTCTCCGGGTGCGGCCCCGCTGCCCCAGGAGGCGGCCCTGGCGCGACAATGGGCCGCTCTGATTCCCGGGCCGGCGCTTTGTTGGAGGGCGGGGTGGCGGGCTCCGCAGCTGTCGCTTTTTCCCACGATCCGGGGAGCTGAGTGTGGCCACCCCCTCCCTCCTGCGGCCCCCTCGTATCTTGTGTTTGAACTGAAGCAAGGGTGGAGGTTGGTCGGGGGCTTTTTCTGGGCTCCTTAATCCACTCCCACTTCGACTGCGTGGTTAGAAGTTTGGGAGAATTTCCTAAGTTTTTCTGTTGCCGTCCACTTCGCCTCACTGTGAATGGGGCTGTACACCTGCCACATAGCCAGCCTATCCCTTCCCCACTAGTTTTTGACTGCCACGCTGTGAGCAGAACATTGATCCGTAAGGGCTACCCAGAAGCTCCCCCTCCCACGCTTCACCTCCGGACTGCCAGTAACTCTAGTACATAGGCACCATGGCTTTAGTCTCCGTCCACCGGCAGGACCGAGACTGACCTCTCTCTTCTGACCCTTTCCCAG
Seq C2 exon
GCTTGAGATGCTCCCAGCCAAGTGGGACCTGCCTGAATGGAGGGAGGTGCGAAGTGGCCAACGGCACTGAAGCCTGTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCGCAGTGAAGGAACGAG
R:
GTTGGCCACTTCGCACCTC
Band lengths:
319-1824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]