DreINT0105462 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65003444-65005015:-
Coord C1 exon
chr5:65004868-65005015
Coord A exon
chr5:65003542-65004867
Coord C2 exon
chr5:65003444-65003541
Length
1326 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGA
5' ss Score
5.24
3' ss Seq
GTTTTCTGTTTGCGACACAGGTA
3' ss Score
8.25
Exon sequences
Seq C1 exon
ATTTTGATACGGAACCGCGCCACAGATCTAGACGCCCGCATGCATGATGGCACCACACCTCTGATACTGGCCGCAAGACTGGCGGTCGAGGGCATGGTGGAGGAACTCATCAACTGCCATGCTGACGTTAATGCCATTGATGACTTTG
Seq A exon
GTATGACTATTAGACTGCCGTGCATCATTCACTCTCTCAGTTATAGTAAATGTAGCTACACTACCAGTCAGAGGCTTTACGCATTATTTTTATTAGCATTTCTTTATAGGTTTTGTGAATGCTCTCATTGAAAAGAGTTTTTATTGTGTTCTTTTTCAGACAATGAAAAATTGTGGTAATTAATTATTATTATTATTACTATTATTATTATTAATAATAATATTTTATTATCACTATTATTGTTTTTGTATTATTATTATTATTATTATTATTAATAATAATATCATCATCGTTATTATTTTATTATCATTATTATTATTATCATTAATAATAATTTATAATCATTATTTATTATCATTATTATTATTATTATTTCATTAATATTATTAATAATATTATTTTATTAGTATTATTTTATTATCATTATTATTATTATTCCATTATCATTATTTTTATCATTGTTATTATTATTATTTTATTATCATTATTATTACTATTATTATTTATTATTATTATTTTATTATCATTATTATTATTATTATTTGATTAACATTATTATTATTATCATTATTATTATGATTATTATTATTATTATTTGATTATCGTTATTGGTATTATTTTTATTATTATTATTATTATTAATGTTAATATTATCATTATTATTATTATTATTATTATTTTTATTTAATACTTATTCTATATTATACCAATCCAAAAGTGAGTGAAGAGATTTGTGAAGTGTCAGAAAATTAGAACATTTGAACATTTTATTTACTATAAAATGCTGAAAAAAATAATTAAAATGTAAAATAAAAAAAACATATTTAAAAAATGTAAGCAGTTGAATTATTCTTAACACTGATGATAATTATAATAAATGATTCTTTAGTATCAAATGAGTATATAAGAATGATTTTTGAATAATAATGTAATAATCAGGAATAAATTACATTTAAAATGTAAGAAAATTGTAGTTGACTATTAATATTTGTCTTTTTTCAATATCTTTCTTTTTTTATATTTATTTAATTTAATTTCAGTATTAAACAGTTTAAAATGCAAGTAAAGACATTTTTAATGTTACATAAAATGCAAAAAAAATGTAATTAAAATATCCTGAAAAAGTATTAGTTTCCACAAAAAAAAACTGTTATTTACTTCTGTCTTTATTTTATTTCTTTGTTAATTTTGATGGCTGGTGGAATATTTTTTTGTGAGAATTAAGCCAAGCATCATTAAACGTCTAATTTGTTACTATATTTAGTTTTTCTCCTCAAATGTACTGTAATAGAGCACATGCTGAAGTGTTTTCTGTTTGCGACACAG
Seq C2 exon
GTAAATCTGCTCTTCACTGGGCAGCAGCTGTGAACAATGTAGATGCAGCGATGGTGTTGCTTAAGAATGGGGCAAATAAAGACATGCAGAACAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:32
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=0.212
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PD(14.4=26.0),PF127962=Ank_2=PU(31.2=58.0)
A:
NA
C2:
PF127962=Ank_2=FE(34.4=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:
ATTTTGATACGGAACCGCGCC
R:
TCTGCATGTCTTTATTTGCCCCA
Band lengths:
238-1564
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]