DreINT0105516 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53280482-53282350:-
Coord C1 exon
chr3:53282218-53282350
Coord A exon
chr3:53280737-53282217
Coord C2 exon
chr3:53280482-53280736
Length
1481 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAAT
5' ss Score
4.69
3' ss Seq
TACTTTTTACCTTTTCTTAGGTG
3' ss Score
9.07
Exon sequences
Seq C1 exon
TGTATGCCTGGTTATGAGGGAAACAACTGTGAGAGAGAGGTCAATGAGTGCCAGTCTCACCCATGTCAGAATGGAGGAACCTGCATCGACTTAGTGGGACATTACATCTGCTCCTGCCCTCCAGGAACACTGG
Seq A exon
GTAAATTTTTTTCAAATTTATAAAATGCAAAATAAAAATTAAATCAGAAGAGTTTTTACTTATCTGTTGTACTAGTATTTACAGGGTCCCCACGGGGTCTTAAAAAGTGTTAAAAAGTCTGGGGAAAAAAAAAAAGAGAGAAAATTTTTTTGAAATTTATGGCTTTAAAAAGTCTTAAATTTGCTGTTCTTGGTCTTAAATATTTTTGCACAGGTCTTATTTTTGCGATGTCCAAGTAACGCTACATCTAAAGCTCATTTAAATTCTTTTTGTTGTTGTTGCTTTATTTGTTTTTAGTTCTTTATTTCACTAGTCCAATTGTAATTTGCGGTATTACAACTACAAAAAGGTCAACTTGCAATAGCCAATCAGCTTTCTGATATTAAACTCAGTGCGGGCAGCGAATGTGACATCATCGCTGTGTTTGCGGAAGTTTGCTTTGAGTGCGCGCGACATGATTTCGCCTGGCAGAGTATGCCGTTATTTCACTGACAAATGTCGCAAGCGCAGTTTTATAAGTCGGGAGCGCTTTAATACGAGAAAGCGAATCTCTGCTCACGCGCCGGTTTCCTTTAAAAAAAAAAACTAAAGCACTGGGTAGTTTGTTTTTAATACGCTTGTTGTGTTATCATAGCAACTATAGTATTACCACAACAGAGTAATTGAAGTACTTTACTGTACTTTACAAAACACTGTACAGCAGACACTAGTTCACTTTATTTAAGTGATAAAATGGGATTGATAGTGGAATTTATTTGAAGAGTGAATAGTACAGTAGGCTATAATATATATATATATATATATATATATATATATATATATCTACCTAATCAAGCTTTTACCTATTTTCTATCACAGTTACATTTCTGCTTGCCAGAATGACCAATAATTATTGGCTAGAAATTGCAACAGCCATGGGAAAGGGAAAAGTTTTTGTAAAACTTTGGAAAAACCTGAGGGATAAGTTTGTTAAAACAACAAAAAAAGGCCCCCAAAAACATCTTCAATGATAATGATTATCTTTTTATTCGTCTGATTTTACTTTGTTTTTTTGGACCGCCCCCTGTCATTTAAAAAAAATATCTTAATGGTGAACGTGTCAAGTATAAAAGCCCTAATCCATTTCGTGTGTTGTGCGATGCGGTGCCAGGTAAAGGTATAAATCTGCATTAAGATGTTTTCTGTAGTTCAATGGTGCATTTAACCTGACTTTAGTACTGTTCAATTTAAATAACTTTATTTTACCCCTAATTTTGTGTGTTTTTGATATTGCGATATAGGTCTTAAATTTAATACTTAATGGTCTCAAAAAGGTTGTAAAAGGTCTTAAATTTGACATTATGATATCTGCAGAAACCCTGATTTATTACTGTTAGGTTACCCATTTGATACAACTTTTTTAAGTTTACTGACCACAAACATTTGAGCAGTATTATACATACATTGGAATGAAGTACCTATTACTTTTTACCTTTTCTTAG
Seq C2 exon
GTGTACTCTGTGAGATAAATGAGGATGATTGTGCAACTCCCTCATGGCCTCGGGGAATGCCCAAATGTCAAAATAATGGCACATGTGTGGACAGAGTTGGAGGGTACAGGTGTAACTGTCCTCCAGGCTTCACTGGAGAACGTTGCGAGGGAGACATCAACGAATGTCTTTCCAACCCCTGCAACCCCTCAAACAGCTTGGACTGCATACAGTTGCCCAATGATTACCAATGTGTGTGCAAACCTGGCTTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:21
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(25.8=17.8),PF0000822=EGF=PU(84.8=62.2)
A:
NA
C2:
PF0000822=EGF=PD(12.1=4.7),PF0000822=EGF=WD(100=39.5),PF0000822=EGF=PU(90.9=34.9)
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:
CAATGAGTGCCAGTCTCACCC
R:
AAGCCAGGTTTGCACACACAT
Band lengths:
342-1823
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]