RnoINT0102228 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3905453-3909857:-
Coord C1 exon
chr3:3909760-3909857
Coord A exon
chr3:3908593-3909759
Coord C2 exon
chr3:3905453-3908592
Length
1167 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CTCCTGTCCATTACCTACAGGAG
3' ss Score
8.85
Exon sequences
Seq C1 exon
GCAAGTCAGCTCTGCACTGGGCAGCCGCTGTGAACAATGTGGACGCTGCTGTTGTGCTCCTGAAGAACGGAGCCAACAAAGACATGCAGAACAACAAG
Seq A exon
GTAAGCAGAGGGTGTGCCTGAACCACAGGGGTAGGCCAGGGACTCCGTCTGGTGCACCCATACGTTGGCCAGAGTGTGAAGAGTGTCTGGGACGCAGCTAGCTTTTCTGACTTGTCCAAGAGTGGGGACTGGAGCAGCAGATAAAATAACCCATGCCCTTGCTGGAGAGGAGATGAGGCAGCAGCTGTCTTACGTCACTGTTAATTGAGCCTTGCCTTTTGTTCCCTTCTGTCCCTGGGGGTGTGTGGTGACCTTAGGGGCTCAGGATCGGCCAAGGGCAAGGATGGGGTGGCCCTGTCTCTTAAGGCCTGCAAGGCCCCTGGCCCACTCACTGCTACCATCGTCCTTCCTTTGGGATAAGGAACTGTACCGAGCTGGGCCGCAGCCTTGCCTCCCGGTGTCACTGTCTACAGGGCTAGTTGTTTCTTCAGGACTATGCGTAGTTACTCAGAAGGGCAGAGTTTGGGCCTCCCTTACCAGGTCCACTGCAGGCTGGGACGTGCACCAGGAGTCTGGCACCAGGTTCCCTGCAGTCCAGGGTGGGCCTAGTAGACAGTTCTGTAGGCTCCTATGCCCTTTGCACTCCTCACAGAGAGTCATATGACTATGTCTACTGGGCAGAGCAGACCAGAAGAAGCTGAGATGCCTTAGCCACCAGGGACCCTTTGGACAGGAAGTACCTTCCCCACGTCCATTCATTTGCCTTATGGGTTCCTGAATCCCAGGATTGCAGATTCCGTACCTGCATTTTTGGGAAGGAGAGCTAAAGGCACATGGTTCATTAAGTTTCTTGGCAGCCTGACGCCACACAGGGGAAGCCCTATGGATTTATCCCACAGACCTTCTCTGGGGGTGTGAGGAGATAAATCTAGGTTCTCTAAAAAAGGACTCAGGATCAGCCGGGTGTGTTTCCTAGCACCAGGAAGCTAAGGCAAGACGATACTGGGTTCCTGGCCACTCCGGGTAATATAGGGAGGCCCCATGATAAACCCTCTTCTCCCCCAGCCGGGTCCGCTAGGGTGTTTGGTCTAGATAGGTCTCTCCCTCTGTAAGGAAGCAGAAGCACTGCTTCCCTAGCCCCTCCTCCCAGGCCATCCATCATAGATGGCTCAGCGAGTTCTACGCCAGGCCCAGCTCCCTCATGTGCCTCCTGTCCATTACCTACAG
Seq C2 exon
GAGGAGACTCCCCTGTTCCTGGCCGCCCGTGAGGGCAGCTATGAGACTGCCAAAGTGTTGCTGGACCACTTTGCCAACCGGGACATCACGGATCACATGGACCGATTGCCACGGGACATTGCACAGGAGCGCATGCACCACGATATCGTGCGGCTTTTGGATGAATACAACCTGGTGCGCAGCCCACAGCTGCATGGCACTGCCTTGGGTGGCACACCCACTCTGTCTCCCACACTCTGCTCGCCCAACGGCTACCTGGGCAACCTCAAGTCTGCCACACAGGGCAAGAAGGCCCGAAAGCCCAGCACCAAAGGGCTGGCTTGCAGTAGCAAGGAAGCTAAGGACCTCAAGGCCCGGAGGAAGAAGTCCCAGGATGGCAAGGGCTGCCTGTTGGACAGCTCAAGCATGCTGTCACCCGTGGACTCCCTCGAGTCACCCCATGGCTACTTGTCAGATGTGGCCTCACCACCCCTCCTTCCCTCCCCGTTCCAGCAGTCTCCATCCATGCCTCTCAGCCACCTGCCAGGTATGCCTGACACCCACCTGGGCATCAGCCACTTGAATGTGGCAGCCAAGCCCGAGATGGCAGCTCTGGCCGGAGGCAGCCGGTTGGCCTTTGAGCCACCCCCACCACGCCTCTCCCACCTGCCTGTAGCCTCCAGTGCCAGCACAGTGCTGAGTACCAATGGCACAGGGGCTATGAATTTCACCGTGGGTGCACCGGCAAGCTTGAATGGCCAGTGTGAGTGGCTTCCCCGGCTCCAGAATGGCATGGTGCCCAGCCAGTACAACCCGCTAAGGCCAGGTGTGACTCCGGGCACACTAAGCACACAGGCAGCTGGCCTCCAGCATGGCATGATGGGCCCGATACACAGCAGCCTCTCCACCAATACCTTGTCCCCGATTATCTACCAGGGCCTGCCCAACACAAGGCTGGCCACACAGCCCCACCTGGTGCAGACCCAGCAGGTGCAGCCACAGAACTTACAAATCCAGCCTCAGAACCTGCAGCCACCATCGCAGCCACACCTCAGTGTGAGCTCAGCAGCCAATGGGCACCTGGGTCGGAGCTTCCTGAGCGGGGAGCCCAGCCAGGCAGACGTACAGCCGCTGGGCCCCAGCAGTCTGCCTGTGCACACCATTCTGCCCCAGGAAAGCCAGGCTCTGCCGACATCACTGCCATCCTCCATGGTCCCACCCATGACCACTACCCAGTTCCTGACCCCTCCTTCTCAGCACAGCTACTCATCCTCACCTGTGGACAACACCCCCAGCCACCAGCTGCAGGTGCCAGAGCACCCCTTCCTCACCCCATCCCCTGAGTCCCCTGACCAGTGGTCCAGCTCCTCCCCGCATTCCAACATCTCTGATTGGTCCGAGGGCATCTCTAGCCCGCCCACGAGCATGCCGTCCCAGATCACCCACATTCCAGAGGCATTTAAGTAAACAGAGATGTGGGATGAAGGACCCCAGCTTCCGTTCCCAAGCTCTGTTGGGAGTCCTTTCCAGTGCTCCAGGATGCTGGGGCGACCAAAGGAGCCTTTTAAAAAAAAATGTTTTTATACAAAATAAGAGGACAAGAATTTCCATTTTTTTTTTTAGTATTTATTTATGTACTTTTATTTTCCACAGAAACACTGCCTTTTTATTTATATGTATTGTTTTCTATGGCACTAGGGGAAAACATCTGTTCCAAGAAAATAAACTAGTTCTGAGAGCCTCGATTTTCCTGGTCAGGGTGAAGTTCCCTGTGTGTTTGTAAAATACGAACAAGGATTCATGATTTGTAAATGCCGTTTATTTATTGATTGCTTCTTTCCAAAATCGTCGAGAAAGAAAGAAAGAAAAAGAAAGAAAGAAAGAAAGAAAGGAAAGAAAGAAAGAAAGGCATGCTAGGAGAAAGGAGGAGGAGGCTGGAAACTTCCTCGCCAGATTTCCCCCTCCCCAGATGCCTGCTACCCCACTCACTGCCCCTCCTCCCAGTGTCACCTGGGATTTGCAGATGTGTTTAGAAACAGGCCAAGACCTTGAACCTCGGGTACATGGATTAGTTTTGTATCTAAAACAGGAAACAAGTAAAATGATGTGGTTTGTACATTTTCTGTAACCACCGCATGGGCTTGGAGAAGTGTCCTCGGTGTGTGTGGAGTGTTCTACCCAGTACCAGGTATGAATCTGCAGGCTTCAGTGTTCTGTACTAGTGTTTATGGCCCTTGGGAGTACTACTCCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCAACTGTCCCCTTCCTGACATCTTGAGCCAGTAAGCCAAGTGGGGTGTGGTGCCTCCTGGAGAATGACACTGCCTGGACTGTTCCGTGCGTCACCCCTGAACAGCATCATCCAAATTCAACTGAGGATGGACTGTCCCTGCCTGGGCCTGGGCTCCTGACATCCGACTGCCAAAGGGCTCCAATGTGCACTGTGAACTCACCAGAGCAGCCTACATTGAGACCTCAAGAAGATATAAGCTGTGTGGCCTCTGATCCCCCAACTGGCCTGGGTGGGGACGTGCCTTGAGTGTGCTGGAATGTGGGCGGAGCCTGCCTCTGGGCCACCCCTCCTGGTTCAGGGCGGTGCTCACAGCAGATTTTTGCAGTATCAAGTATACGCCTGTGGCAGAATAAGTATCTGTAAATACATGTTTAAAGGTGGATTTTGTTTAAGAAATCTAAAGGAACAAGTCTGTCCCGTGTCAAGCTGATGAGGAATGTCAGACCATGGCTCAGCTCGGTGTGACCCAGGCCTTGTGACCTGACAGTAGCTCCTAAGAGCACAACCCAGGATGGCCCATCTGCTGTCCACCAAGCCCTTTCCCAGCCACTGTGTGCGGGGAGGGGGGCTTTCGGGGGCAGCTGCCTACCTCCTCAGGGCAGCTCCTCCTGGCCTTTTGGGAAGCAGTGTCTGCGCTATACCTAATAGATATGACCAGACACATCCTAAGATGTTGATTCTTACTGTGTTTTATTAAAAAAAAATGTAGTTTACAGAAAAAAGAAACTTAAAAAAAAGTTATCTACATGTAAAACTGTAGGTAATAAAAGTGATGTATTTTTTCATCTTTTTTGTTAACTAATTTGCAATAAAAATGAAGCTGATGGTCTTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.212 A=NA C2=0.778
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(31.1=84.8)
A:
NA
C2:
PF127962=Ank_2=PD(66.7=12.4),PF119363=DUF3454=WD(100=13.5)
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:
AACAATGTGGACGCTGCTGTT
R:
TGTGTGGCAGACTTGAGGTTG
Band lengths:
347-1514
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]