DreINT0105525 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53291270-53291831:-
Coord C1 exon
chr3:53291689-53291831
Coord A exon
chr3:53291606-53291688
Coord C2 exon
chr3:53291270-53291605
Length
83 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GATGTTTCTTCTCTTTACAGGTC
3' ss Score
12.79
Exon sequences
Seq C1 exon
ATGCCGGCCTGGTTATATTGGTTCGCTCTGTCAGCATCTGGATCCCTGTCACCGTTCGCCTTGTCTAAATGCAGCAGCTTGCAAGAGCCAAGTGGCGAATTCAATCCCTCAGTACACCTGTGTGTGTCAGCGAGGCTTTAGAG
Seq A exon
GTAAGCTTAGTGAAGCCTTCACGCCTTCGTGGTAAATTTTAAGGAAATTATAGCAGGTTTGTTGATGTTTCTTCTCTTTACAG
Seq C2 exon
GTCAGGATTGTTCTCTCGTTGATGCGTGTGCCACAAGTCCTTGTGCCAATGGTGCTCGTTGTACCAATTGGAATAATCACTACAACTGCTCATGCCCACCTGGGTATCAGGGAAAGAACTGTCGCAATGATATTGATGAGTGCCGCAAACCCGGAAAGTGTCTTAATGGTGGCATCTGCATGAATACACATGGCTCATTTCGCTGTGAGTGCCTTACAGGGTACAGCGGGCGCACATGCGAGGTGCCCACCCAGCCCTGTGCCCCATCACAATGTCTCAACGGCGGCACCTGCCATCAGACCGGTGACCACACCTACGAATGTGCTTGTTTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:3
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(31.0=18.4)
A:
NA
C2:
PF0000822=EGF=WD(100=27.4),PF0764510=EGF_CA=WD(100=38.9),PF0000822=EGF=PU(81.2=23.0)
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:
TGTCAGCATCTGGATCCCTGT
R:
TGGTACAACGAGCACCATTGG
Band lengths:
181-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]