DreINT0105455 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65017049-65017804:-
Coord C1 exon
chr5:65017370-65017804
Coord A exon
chr5:65017198-65017369
Coord C2 exon
chr5:65017049-65017197
Length
172 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
ATTCTTATGTTTCCCATCAGCTC
3' ss Score
7.3
Exon sequences
Seq C1 exon
TCCACTATACGATCAGTATTGCAAGGACCACTTTGCAGACGGCTACTGTGACCAGGGCTGCAATAATGCAGAGTGTGAATGGGACGGCCTGGACTGCGCTAACGACACCCCCGAGAAGCTGGCTGCAGGACTGCTGGTTGTGGTGGTCCACATTCACCCTGATCAGCTCCGAAACAACTCGTTCGGGTTTCTGCGGGAGCTCAGCCGAGTGCTCCACACCAACGTGGTTTTCCGGCGGGATAGCAAGGGGCAAGAAATGATCTACCCGTATTACGGCAATGAGCAGGAACTGAAGAAACACAACATCAAACGATCACTAGACGGCTGGAACGATGCTTCTAGCGATGTCTTGAGCTCGATGAAAAACAGCATTTACAATATAGTAGTGGAAGGAGGGAGAAAACGCAGAGAACTGGAGAAGATACAAGTCAAAGG
Seq A exon
GTAAGTGTGTGTGATATAAAAAAATGTCGGAATAGTTGGCGGTTCAGTCCACTGTGGGGAAAATTGAATTAATAATTCAAAGCGGCATATAAACATTTGCTGTCGTGACTTTTTGTCAGATTATTTCTTCAAGACATGCTTTAATAAAATCAATTCTTATGTTTCCCATCAG
Seq C2 exon
CTCCGTGGTTTATCTGGAGATTGACAACCGGCAGTGCTACCAGCAAACCTCCGAATGCTTCCAGAGCGCCAACGACGCGGCGGCGTTCCTCGGAGCGCTGGCTTCCAGCGGCAGTCTGAAAATGCCTTACGTCATCGAGGCCGTCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:26
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:
PF0006612=Notch=PD(82.5=22.6),PF068168=NOD=WD(100=39.0),PF076847=NODP=PU(4.8=2.1)
A:
NA
C2:
PF076847=NODP=FE(79.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACTAGACGGCTGGAACGAT
R:
TTTTCAGACTGCCGCTGGAAG
Band lengths:
244-416
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]