DreINT0105456 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65015994-65017197:-
Coord C1 exon
chr5:65017049-65017197
Coord A exon
chr5:65016208-65017048
Coord C2 exon
chr5:65015994-65016207
Length
841 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
AACGGTTGTTCCTGTGGCAGGTG
3' ss Score
7.38
Exon sequences
Seq C1 exon
CTCCGTGGTTTATCTGGAGATTGACAACCGGCAGTGCTACCAGCAAACCTCCGAATGCTTCCAGAGCGCCAACGACGCGGCGGCGTTCCTCGGAGCGCTGGCTTCCAGCGGCAGTCTGAAAATGCCTTACGTCATCGAGGCCGTCACAA
Seq A exon
GTAAGCGTTCGGCACGAGCATTGTCGTGTGCCTCACGTCTTCCCATAATGCCTTTAATCAACACTAGGCCTCCTATCTTACTCAATGTATTCAATACCAACCCCCCCATCCCCAACCTTTAACCCCACCGCCTCCTACCGCGGATTACAGGGATCGCTTTGAAGTTTGTAGCGTTTCTTCCTTATAACAATGAAGCAAGTGTTCTTTGTGCATTAGACAGACTAAACAATCAATGCACTGGTCTGAGGGCAGATCTGCTTCCTCCAGGCAACCCAAAATAGTTAATTGATGCAAATCATGTCAACTCGTTTGGCTCAACATGACACATACATGCATGGCGTGAATGTGAAATGATGGGGGGGCTGCCGCAACCTTAACCTAGTCGAACGTAGCAGGACTTAACGCATCTCCAAGGGTTTAGATGAGCAGAGTTTATCATTTCAAAATCGTTAGTGGAGAGAGTGTGGAAAAAAAAAGAGAAGAGTGGAGAAAAATTGATCGGGAGTGTGCTAGAAGTTGGGAGTCTTTGTTATCTGGAAAATCCTAATAAATCCTTCGTCTTTACAGCTTAAAGTGTGCGCGGTAATTTGAAGTTCATTAATCCCTCCCTTTTTTTTCCCTTAAAGAAGAACTGGTAAAGTTGTCTCCTGGTACCCTGGGCTGAGAAAAAGGGAGAGGAGGTGTTCATTCGTTTTTTTTTCCCCGTCCTCCTCCTTTTTTCTTATTTGCCAGCTTTTTTTGATGAGAAGCGGTTAGCAATTCTGATTACCGCATAGTTTGTCCGCCCATCTTCGGAGCATATTCTTGACTCTTGACATGTCAACGGTTGTTCCTGTGGCAG
Seq C2 exon
GTGAGATCGATGGACCGTCGCCTGTAGAGCTCTATCCAGTCTACGTGGTTCTGGCAGGATTGGCGCTGCTGGCCTTTGTCGCCATTGGGATGGTGGCGTCCCGTAAACGGCGCCGGGAACACGGACAACTTTGGTTTCCGGAGGGTTTTAAGACCAGCGAGCCCAGCAAGAAGAAGAGGAGAGAGCCGGTCGGAGAAGATTCAGTCGGTTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:27
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=0.361
Domain overlap (PFAM):
C1:
PF076847=NODP=FE(79.4=100)
A:
NA
C2:
PF076847=NODP=PD(14.3=12.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAGATTGACAACCGGCAG
R:
CGACTGAATCTTCTCCGACCG
Band lengths:
343-1184
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]