DreINT0105440 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65042089-65045319:-
Coord C1 exon
chr5:65045209-65045319
Coord A exon
chr5:65042282-65045208
Coord C2 exon
chr5:65042089-65042281
Length
2927 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GGTCTGATCTTATTTTGTAGGGA
3' ss Score
8.1
Exon sequences
Seq C1 exon
GAGCTAACTGTGAGATCAACCTGGATGACTGTCAGAGCAATCCCTGTGATTTCGGGAGATGCATCGACAAGATAAATGGGTACGAGTGTGCCTGCGAACCGGGATACACAG
Seq A exon
GTGAGTGACATTGCATCATGTGATGTTATATCTGAATTGACAGAGGAGGGAAATTGTAATCATTATTTATTGTAGGAGTAGGTGGGACACTCAGAAATAAAGGTATAAAATCTGTCACTGTGATGGCACCTTTTCTAAAGGTACACTTTTGTACTGTACAGGTCGACAGTAGTACCTTTAGGGTACACTTTTGTACCTTTAAGATTCACTTTATGAAGTTTATTTATGAACTTATTTCGAGAGGATCGAGTGCTTATGATTGCTCACAGCTGGTCCCACATCAGCTCACGATTCATTCGCCAATCAGATGTCTTCTAACTCACTATAAGTAACCAGAGTTTTCTTATAGCAGTCTCTTCGTCTTTAAGAATCACCCCCCCCCCCTCCACCCCTACTCCCCCATCTTTTCAGATGGGCGACACGGCGGCCCAGTGATTAGCACTGTTGCCTTACAGCGAGAATGTCTCCAGTTAAAATCCCTACACTGTACAAAATGCAGTTCCACACAATTCATTCATGCTGTCCCAACACAAATTGATTAAGTTAACTTAACAATTTTTACAAATTTATGTGGATTGAACATAAAAAGTTAGGTTGTCCCAATGAAATTTCAAGAATTAAGTAAATTGAACATACCAAATCAATACCATAGCCAAGCTCTAAACAAGTGTACATCTCTTCTTAGCCATTCTATTAGCCAAAAATAAGTCGGGGGAGTTCATCGAAAAAATTGAATAAATAAATGAATTAATTATATTAGTGCATACTAATATACTCTGAACTGTAGTTGCTGGTTAATAACAATCCCAATTTGACATTTTAGCTTGTGCTATGTGACTGTTGCGGATTTGCATATTGCGATATTGATGCTGAAACGATGTGAAGTTTATTTATAATTATTTATCACGTGCTTATGATTGCTTGCGGCCAGTCCTGCATTATTCAATTTATGATTCACCAACCAAACGATTCCTAAGCCACTATAAATACTTTAAGTTCCATATGACAGCCATCTTCATTTTGGAGAATCCCGCCCTTCCACCCCTACTCCTCCACCTTTCCTAGATGGGTGACACAGTGGCCCAGTGGTTAGCACTGTTGCCTCACAACAAGAACGTCACTGGTTCTAGTCCTTACCAAGCCAGCCGACGTTTCTGTGTGGAGTTTACACGTTCTCCCCGTGCTCACGTTGGTTCACCCCGGGTTCTCCAGTTTCCTTTCATCGTCCAATAATATGCGACTTCGGTTAATTGACTAATCCAAATCGGCACCATAGACATGCTCCTAGTAAATAGTTATCCTTTAAGAGCAATCACTATCTGTTCATTAGCTACTACAGCAGGTGAGTTCTCGAGATCTACCTGAGCTCAAACTCCCCTCTCGCCTTGCAAATGGGAGGGAGCCCCGGGCTTGAGGATCTTATGAGCTCAGGGCTCTCTCCTGAGAAAAACAAGCTTCATAATCAATCATCAGCTAAGTGTGAACTCTTGCAATATTGTGCAGCAATATATATATTGTTTGGGTTGGTGTTGTATATCACACTCAAAAAACTGTATATTTTCTGTTTTTTAACTGTCTTATTTCACTATATATTATTTATTATATATTATATTTTTCAAACTACTAAAATGTCAGTAAATGTCACTTTGTTAAACTGCAGAGTTGAATTTTCAGCAATAAAAGTTGGCAGAGCAGTGATCAACATCCCATAATGCAATTCACAACCATAAATAAATCCAAAATACGCAAAACAAAATACGGAAACTGTTAATTAACAGATTTTTTTTTTACTATGTAGATCCTTTAGAAATCAATAGGAATACCGGAATTCATCCTATTTTCGTCTAAATTGATTTATCCTTAACATCTGGGATTTGAGACTAAAAATTAAACATCAAAATCTTCAGAAAAGCCATTGTGGAAGTCAAGTCTAGGTGGTACGGTAAGCCCAGGTCTTTACCACTGCAGATGAGATGGCGAGTCAACAAAGAGTTCAACAGGTGAGACGGGCCACAAAAGCAGTGTGGGGAGAGACAGCTGGCCAGCGAGCACACACTCCGGTCTGGGCCGCGGTGTTGGCTTACAGTCTCACCCAATCCCCGCCTGCTGTGCGGCCCGCTCCCCCATTCAGACCCAGATCTCCAGGACATCTGGGAGTTTGAAAGGAGAAAAGATTTGCCAAAGATTTGTGAAAGTCGATCTTTTAAAAGGGGGAATTTGGCCGGTACTTTAAAGACAAGTGACAAACGAAACCTCTACCTTTATGCTGGGCATTGCGTTGGGTGAATAGTGCTGCTGGAATAGTAAGCTGGGCCTTAAAGGGATAGTTCACCCAAAAACTACAAATCTGTCATCATTAACTTTAATACTACCTTTATTTCTTTCAAACCTTTATGGGTTTCTTTCTTCTGTTGAACACAAAAGAAGTTATTTTGAGGAAAGCTGAAAACCTGTAACCATTGACTTCTTGTTTTACCTACTATGGCAGTGTTTCTCAACCACGTTCCTGGAGGACCACGACACTGCATGTTTTTGGATGTCATACCCATTACAGGTCTTTCAGTGTCTGCTAATGAGCTGATGGTCTGAATCCGTTTGGTTAAGGATACATGGAAATGTGCAGAGCTGGTGGTCCTGCAGGAACGTGGTTGAGAAACACTGTACTATGGGAGTCAAAACCTACGTTTTTTTCAGCTTTCTTCAGGATATCTTCTTTTGTGTTCAACAGAATAAAATACACACAATGGTTTAGAACCACTTAAGTGTCAGTAAATAATAGATAAATTGTGTTTTTGTGTGAACTATTCCTTTTAGGCCTAAAATTTTAAATGAGGAGCCGGCAAATTAATCCAATCGATACTGAAGGTATTTTGAATAACTTTGAGTAACACTATGCAAAGTTTTCATGGTCTGATCTTATTTTGTAG
Seq C2 exon
GGAAAATGTGCAACATCAATATCGATGAATGTGCCATCAACCCCTGCCACAATGGCGGAACCTGTGTGGATGGAGTCAATGGCTTCACTTGTCTGTGCAGAGAGGGCTATCATGACACCACCTGCCAATCACAGCTCAACGAATGCCTCAGCAACCCCTGTATCCATGGACACTGTGAAGACAAAGTCAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:12
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=PD(6.5=5.3),PF0000822=EGF=PU(93.1=71.1)
A:
NA
C2:
PF0000822=EGF=PD(3.4=1.5),PF0000822=EGF=WD(100=47.7),PF0000822=EGF=PU(53.3=24.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]