DreINT0105528 @ danRer10
Intron Retention
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53275051-53276999:-
Coord C1 exon
chr3:53276902-53276999
Coord A exon
chr3:53276814-53276901
Coord C2 exon
chr3:53275051-53276813
Length
88 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
TTTCCATTTCTGATCTTTAGGAG
3' ss Score
9.18
Exon sequences
Seq C1 exon
GAAAGTCAGCATTGCACTGGGCAGCAGCAGTCAATAACGTTGAAGCTACTATTGCCTTGTTGAAGAATGGTGCCAATAAAGATATGCAAGACCTCAAG
Seq A exon
GTATGCAGTCATATACTTTTGTTTTGAAGTTGTTTTTTTTATATCCACTTATACCATGTTATTAATTTTTTCCATTTCTGATCTTTAG
Seq C2 exon
GAGGAGACTCCGCTGTTCTTGGCTGCCAGGGAAGGCAGCTGTGAGGCAGTAAAGGTGTTGTTGGCTCACTTTGCCAATAGGGAAATAACAGATCACATGGACAGACTCCCTCGAGATATTGCCCAGGAGCGCATGCATCATGACATTGTGCAGCTACTGGATGAATATAACACTGTGCGAAGTCCACAGGGTCATGCAGGGGCAGGTCACCACCTCTCTGGTAGCCACACACTCTCACCGCTCATGTGCCCTCCCAGCAACTTCCTCCAAGGGCTGAAAAGTACCCCTCAGGGTAAGAAGAACCGTCGCCCGGGAGCTAAAGGCATTGGTGGACAGCACGCTTCCGGCCTGAAAGATTCAGCCAAAGGACGCAACAAACGGCTGACTCTAGACATGCAGAGTGCTTTGCTGGATAGCTCTGTCACGCTCTCCCCTGTTGACTCACTGGATTCACCACGTGGAGGCGCCAGTAACGCTGGCTACGTCACCAATCCAACCTCACCAGCTGCCATGCCCTCTCCCGGCCTTTTCCACTCCTCTATGTCTGTCCCTAATACCCCTATGGTGCACAGCAGTATCCTGGACAGCACCAGCCCTTTTGCTGTCTCCCTGGCACAGTTGAGTGACCTGGGAGATGGTGGGCTCTCAATGCAGGGGCGTGTGGGCATGCAAGGAGGGGGTGTCAACCCAGGCCCCCATAACTACGTGATGAACGCCGGTCAAATGAGCCTTAGTATGGGCATGGTAAGTCCAGTAAGCGTGCCGTTTGACTGGCACAACCGCATGCCTCCATCTTCTCAGTGCAGTCAGCCAATGATCAGCATGGTGCATCCAGTAAGTAGTCAAGCAGGCATGCTCCCACAAACACCAACCCTGCAAAGCAGCATGCTATTGCACCAGCAGGTGTTCCGTAATGCCCAGCAGCCCATCCTGCAGCCAACACCTGTCTCCAGCACACCGTCTATTAGTCCAGTCAAACTGCCTCCCATTGCTGAGCAGCAGCCGCAGCAACTTCACAGCCACACCCTCACCAACCCCAACCTCTCCCGCATGGCCACCTCCACTCCCCCAACTCCACAGCAGGCACAGCCTCCTCCAGCTTTCTACCAACCACAACAGCCACAAGCTCAGCCGCCGCAGGCCCCGACAGCCCCTCAGGCAACGCAAGCACAAGCTATCCCATCTCAGGCACCCCCAGCACAGGTGAGCGGCAGCACCGCAGGCCCAGAGGATTACCCCACACCACCTTCCCAGCACAGCTACAGCTCAGCCATGGATGCAACGCCTAAGCATTATCTGCATGTGCCCAATGAACATCCTTACCTGACCCCTTCTCCAGAGTCTCCAGAGCCCTGGTCCAGCCCTTCCCCTCACTGTGTGTCTGATTGGTCTGACTCCACACCCAGCCCAGCTGTCACAGCTCCTTCTCAAACCCAGATTTCACAAGTCCAGGAGTCCAACGGGAAGATGCAGGTGTTTGCTTGAGCAGCCCAACCTACCTTAAATGTTTGTGACTTTGAAAGTTTAGAGCTGACAATCGTCACTCTAGGGCTTGTGTTTTTAACTTGCCTGTCAGCCCATTTCCAAGATTTTGATTGGATTAGGATTGACTGTTTTGCGTCAAGAAGACCATCTGCCGGTATCCGCAGAAAGAAAGTTAAAGGGAAATTTGTGTTGTCTTAAAAAGAAAAGACAATTTAATGAAGTAAGACATTCTGTCACAGATGGACTTGTTTTTTAATTATTAAAAAAATATATATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139:ENSDART00000073930:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.030 A=NA C2=0.832
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(34.4=100)
A:
NA
C2:
PF127962=Ank_2=PD(32.3=6.1),PF119363=DUF3454=WD(100=12.9)
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:
GCCTTGTTGAAGAATGGTGCC
R:
CCTGGGCAATATCTCGAGGGA
Band lengths:
172-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]