DreINT0105459 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65069644-65072205:-
Coord C1 exon
chr5:65071956-65072205
Coord A exon
chr5:65069983-65071955
Coord C2 exon
chr5:65069644-65069982
Length
1973 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TAAATGCTCTCTATCGCCAGGTA
3' ss Score
8.79
Exon sequences
Seq C1 exon
TACGCCGGCCCAGCGTGCCAGTTCCGCAACCCTTGCTTCCAATCCCCGTGCAGAAATGGTGGCGTGTGCCGTTTGATCACTTCTGCCAACAAGGTGGACTTTGTCTGCAACTGCAGCCTGGGCTACACGGACCGATTGTGCCTCACTCCCACCAACAACGTGTGCCTTGGTGCTCCGTGCCGAAACGGAGGAACGTGCGAACTCACCAGCATCCACAACTACAGGTGTAAATGCCCACCAGGCTGGTCAG
Seq A exon
GTGAGCCCCCAATCCAGTATTAACATCCTTGAAATCAATAATTATTATTAATTTTTGCAAATTTAAAAAATCTGATATGGCAATATTTTGTTTTGCTGTGATTTATAGTGTGATATGGATATGATCTCGTGAATTTAAATCAACTGATGTGATCAAGTCTTTTTATATGCAGTGGATGCACATAATTTATAATAAATTACAAGCAACAATAAATAAATAACCAGTGCTTTATGGGGATTCTAACAGTATTCAAGTACAGAAATTGAACAATTAAGCGTAAAATAACATGATCATCGTTGTGTAAATAATTTTTAAAATATTAATATTTAATAGTATCCTTATCTTTTAATCTCTAATAATTAATTTAGTAATCTAATCCTGCTGTCACAATCACCAGCGATCCAGCATTTGCAGATCACTGAAGAACTACACACATGCCACCACATAAACTACAACTACCAGGAAGCTTTGCACAAATCTACTCCCGCAACAGCTGACAATAATCCAGACAATCACTCACACACACAACTGAAACTCGTGTTGTATGATTACCTGGACTATAAACACAGCACACACACACTTCTGGGCTGTGTGTGTGTGAGTGAGTGTACAGATTATTGTCAGCTGTAGCTGGAGTTGATTTGCGCAAGACATCCTGATAGTTGTAGCTCATGTGGTGGGATGTGTGTAGTTCTCCAACAATCTGCAAACGCTGGATCGATGATGATTGTGACGGCAAGATTAGATTGGACCGCAGACACCGGCGATGTTTCTATTGCAGATGCTCAACATATATATTGTTAAGCCCTAATTTTAATCTACTGATTTTTGAAAAAGTGCTTAAAAATTTTATTAGTTTTAAAACATTTTATAGTTTTTTTTACATAATTTATTTCACTAAATAGATAATCATAATACACTATTTCAATCAAATAAAATCAATCTCTTTGCTTTCGCATAAAATCAATAGCATGTGGTAGCATGAGCTGCCTGTCTTTTTAAAATAAATTAAAATAACTGTAAAATTAAAATGAAAGATAACATATTTTAGATGGATGTCAATGACATTTAAAAAATTAAATAATAGTAATTTAATGTTGGACTTTGGGTAAACATGCCATCAGATATCGCAAAGTGCTAATCTGCTATAGTCACATTGCAGGATGTAAAGCGATTTAAAGTAAATTGAAACCATTTGAACAGTAAACTACAAAGTGTGCCACTTTAACAAAGAATAATTGTTTAATTTTTCATAAAGTGAAAACCATACAATGTTATTTTAAATTCGATTATTCTTTATCTGTACCTTGACACTGTTTCGGTGGAGCTCAGGAGCCACCATAGGCTCATTCTGAAAATGTAGATCGCAAATTATGTAGCCAGAAGTACATATAGCTGCATTTCGTCTTTAAAATGAACGCTACGGGGCGGTGTGACGCCGATGTGGACAGCTTTCCCGCTGTTACTAGTTTGTCCAGTGGCTCGTCGCTTATGTCTCAGACTTGAGACGCCAAAAGGAGTTGAACATGACGACGGGATTCAGTTGGTCAGTCGACAGAGGCTTCTGGTGGCTTTACGCGAGAACAACAGGCACGAATGGCACTCGTGAAAGAAATTTGAGATCTGAAAAAGCGTACACAGCGGCCTCTGGTGCATTCATGAAAACAAACACTGCAAAAAAACGTAGCTCCTGGCACATATTTGGCGCTCTCCAGAAATATAGATACCGGTACGTTTTCAGTATGAGCTTGGGTTGAAAACAAAAGATCGCAATGTCAGTTCTTTTAAATATCTAACGATTAGCATCTGATATAATGAAGTATATATTTTTATATAATTTTCCACAATTGTAAAGTGCTGGAAAAGTTTGGAAAATGCACCTGGAAAATGCTTAAATTTGAAGAAAGCAATTGGGAAAAGTCTACACTAACATCTAAAAGTGTGTTCTGACCTTAAATGCTCTCTATCGCCAG
Seq C2 exon
GTAAAACCTGCCAGCAAGCTGATCCCTGTGCCTCGAATCCTTGTGCCAATGGTGGTCAGTGTAGCCCCTTTGATTCGGACTTCCTCTGCCACTGTACACCTTACTTCTCAGGCCAAACCTGCAAACAAGATGTCAACGAGTGCGCGCAGATTCCCTCTCCGTGTAAGAACGGTGGCGTGTGTGAGAACGGAGTGGGCACGTATCACTGCAACTGTCCCGCCGAGTACACTGGGAAACACTGCGAGAGCCTGTATCAGCCGTGTAACCCCTCGCCATGCTTACACGGGGGCACCTGCGTACAGAAGGGGGAGACCAGTTATGAGTGCTCCTGTCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:3
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:
PF079748=EGF_2=PD(31.2=11.2),PF0000822=EGF=WD(100=39.3),PF0000822=EGF=PU(91.7=37.1)
A:
NA
C2:
PF0000822=EGF=PD(5.6=1.8),PF0000822=EGF=WD(100=27.2),PF0764510=EGF_CA=WD(100=39.5),PF0000822=EGF=PU(81.2=22.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACTCCCACCAACAACGTG
R:
CTCTCGCAGTGTTTCCCAGTG
Band lengths:
356-2329
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]