DreINT0105453 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65020151-65022093:-
Coord C1 exon
chr5:65021981-65022093
Coord A exon
chr5:65020723-65021980
Coord C2 exon
chr5:65020151-65020722
Length
1258 bp
Sequences
Splice sites
5' ss Seq
CCGGTTAGT
5' ss Score
6.1
3' ss Seq
CTTGTGCATGTCTCATTTAGGGT
3' ss Score
8.91
Exon sequences
Seq C1 exon
GTCAGCATTGTGACAAAGTGTTTGATGGCTGTAAAGGGAAGCCGTGTCGTAATGGAGGCACCTGCGCTGTAGCCAGTAACACTCCTCATGGCTTTATCTGCAAATGTCCACCG
Seq A exon
GTTAGTCACATTCTCACACGTCACATCCATAGCACTGGAATTGCTCATAAGCAGTGATCCCTTACTTTAATTTTTGAGCAGAAAAGTCAGGGCCGGCCCATGGCATAGGCAGTATAGGCAAATGCTAAGGGCGCTGTACAGCCAGGGGGCGCCAGAAATGAGCACGGTTAAGTTGGTTTTGTTTTTGATATTCCTGACACATTCAGTGATAGACAGCAATAACTCAAACACCTCCTAGCCTAAAAAGATCTAAAGTGTGTTTCCTACAAAAAGACAAAGCTGGTTATGTTTTACAGCTGTCTTTTTCTTTTCTTTTTCGCTCGACATTACGACGACCACTGCTCCGTTTAGCCGGGGATATGCGTTTTGATGGAAGAGCTTGCGCTGAGCGTAGCTCTCAGTGAGGGACTTTCGGAAAAGTGCTTATTTTTTTCTTCTTTTAATTTTTTTGCTCTGTCCTGCGTGTTTATTTTAAACACAACTAATTTTCTCTTAAATGAGCACAAACAGTTACTAAAGTAGTCGAATGCTTCATTCATTCATTCAATATAGAGCTGTGCATTCTTACATTAACACCTCTGTTATCAAACCAAACACAATGAGAGATTAATTTGCTGATCTTCACTAAATAACTATAGTAACTTTAATCAATATGTTAATACAATTTAAAGTTAAATAGATTTTATAGCTTTATTTATTTCTGTATAAGCCATTGTTTTTAATAGGGTAAACCTTTTATTTTATTCTCAATATGTTCTAATGTTTGCTATGTATTCTATCATTTGAAGCTATTTGTTGTCCCATGTTTTTTACATCCCAACGTTGACAGCTATGGCATAACATTGCTAATCAATAAATAGCTATAGCGCTATCTGTTAGGTTGAACGTCAGCTAATGTTATGGAAGGGCATAGATGTTACAGAAAATAGTAATAGTAATGTAACTACCTTCATTATTACTTCCTCAAGCAAATGTGTAAATATTAGATCTATTCAGCATTAATGTTAATTGCATTGGCATGTTTATCTGACGTTTTCCCAGCTTGTAGTAGTCGATCAAAAAGCTAATTAGTTTCTTATGACTATACACTAGCAGTGGAATTTACTGCGATGTGACGGGGCGCCACCTGAAATCTTGCCTAGGGCGCCAAATTAGTTAGGGCCGGGCCTGAGAAGAGTTAGAGTAACTAATTACACCTCAAAATTTCAGTATAAACCATGATAAAAAAAGTTTTGCATCTTGTGCATGTCTCATTTAG
Seq C2 exon
GGTTTTACGGGCTCGACCTGCGAGTACGACGCTCACGCATGTGGGAGCCTTCAATGCAAAAATGGCGGGACGTGCGTTTCTGGTCACAAGAGTCCCAAATGCCTGTGCACCCCTGCTTTCACTGGTCCCGAGTGCCAGGATCCCAGCGGAGGCCACTGCACCACTAACCCCTGCTATAACGGAGGCACGTGCGAGTATATAACCGAGGAGCCGTATTACCACTGCATCTGTCCCACCAACTTCAACGGCCTCTTCTGCCACATCCTGGACTGGAGTTTTCCAGGCGGCACTGGTCAGGACATCACGCCGGCTCCTAAGGTGTCGGTCAGCTGCGAGATTGAGCAGTGTAAAGTCAAGAAGGGCAATAAGATCTGTGACAGCGCATGTAATAATTACGCCTGCGATTGGGACGGTGGCGACTGTTCGCTGAACTTTAATGACCCATGGAAGAACTGTTCGGCGGCTCTGCAGTGCTGGCGCTATTTTAATAACGGGAAGTGTGATGAACAGTGCCACAACACGGGATGCCTCTATGATGGGTTCGACTGCCAGAGAGTGGAGGCACAGTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:24
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=PU(79.4=71.1)
A:
NA
C2:
PF0000822=EGF=PD(14.7=2.6),PF0000822=EGF=WD(100=15.7),PF0000822=EGF=WD(100=17.3),PF0006612=Notch=WD(100=19.4),PF0006612=Notch=WD(100=19.9),PF0006612=Notch=PU(15.0=3.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTAAAGGGAAGCCGTGTCG
R:
GCAGAAGAGGCCGTTGAAGTT
Band lengths:
343-1601
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]