DreINT0105463 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65000480-65003541:-
Coord C1 exon
chr5:65003444-65003541
Coord A exon
chr5:65002013-65003443
Coord C2 exon
chr5:65000480-65002012
Length
1431 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AATGATTTCCCCATGATCAGGAG
3' ss Score
4.71
Exon sequences
Seq C1 exon
GTAAATCTGCTCTTCACTGGGCAGCAGCTGTGAACAATGTAGATGCAGCGATGGTGTTGCTTAAGAATGGGGCAAATAAAGACATGCAGAACAATAAG
Seq A exon
GTGAGCAGCACTTGATTCTTTTTTATAATGCTATGTTCAGGTAGACAAGGGACAGTTCAGCCAAAACTGAAAATACTGTCATCATTTGGGAGTCCTCCATCTGCCCAAACTTGCATGACTTTGAACACAATAGAAGATATTTTGAAGAATGTTGTTGACCAAGTGGTAATGCGATGAGATACCAAACGCTATGTGTTACAAACCAATAGAAACATTTAAATATCAGTTACTGCATTCCCTATAAGGGTTATAATCTAATTAAACATATTTAACATTATTAAAAGTACATAGGCTGTCGGCGCCAATAGCTTAGTGGTACTGTTCGCCGACATATAGCACAGACATGCTCACAGCGACCTGATTCGATTTCCCAGCTCGAGGTCCTTTGCCGATTCTTCCCCGCTCTTTGCTCCCAATGCTTTTCTGTCTGAAATCTCTACTGTCCTATTATAACAAAGACCAAAAGCCCCTTAAAAATAATTCTAAACAAAAAAATTACATAGGCTGAGTGACTGTTTCTTGTTGGTTTGGACTTACTTTCATTTTCAAACTTCTGCTTGTTATTTTATTTTCAAGATCTGTGGGGAACTACCTGCCACTGCTTGAATGTTACGTAAAATGGTGTTCAAACTCACTTTAGTAACATTTAATACTGAATATAGCACATAATAAGTACCTGAGGTAACTGTTGGTATAGTAGTTTATGGCAGTGGGTCTCAACCACGTTCCTGAAGAACCAGCGCCTCTGCTTATTTCCCATGTTTACTTAACCAAACACACCAGATTCAGATCATCAGCTCATTAGCAGAGACTGAAAGACCTGTAATGGGTGTGACAGAGAAAGGAGACATCCAAAACATGTAGTGTTGGTGGTTCTCCAGGAACGTGGTTGAGAAACACTGGTTTATGGTGTTTTTTTGCCATGATATTTCTAAAATAGACCTTCCGAGTGTTGCAGATGGTTAGGACAAATACTCCTTCAGGATTCGATTGGTGCACAGATTTAAAAAACAAGTTCAGAACATGAAACTATAGTGTCATGGCTTTTAAATGATGCCTTGTTTTTGATACATGGTTGAATATTTTTACTAAACGAAGGTAATAAATTCTACAGACACGCCCAGATGGCCTGTATTCAGGCTGTTGCCAGTTGTTAACCTGGAAAAGCTACCTTTTATTGCATGTCACAGCAGGCATCGAGTGTTAGGACAAAGAAATAGTGTAGCTAGGCACCAAAGAAATATTATGGAAGTCAATTTGGATCATTAACTGTTTGGTTACCAACATTCTTAAAAATATTTGTGTTCAGCTAAATAAGAAACCCACATTATATTGGAATAACTTGGAGTTTGTACATGATTCAGGTGAAAACTATGACAAGAAACCATTTTTATTAAGCTTGTGCCTAACAAATGATTTCCCCATGATCAG
Seq C2 exon
GAGGAGACTCCTCTTTTCCTGGCGGCAAGGGAAGGAAGTTACGAGACGGCTAAAGTTCTTCTGGAGCATTTTGCAAACCGGGAAATCACAGACCACATGGATCGACTCCCGCGAGACATCGCGCAAGACAGAATGCATCATGATATTGTGCGTCTTATTGATGAATACAACCTAGTGCGCAGTCCTCCCATGCACAGCGCCCCGCTCTGCACCACGCTTTCCCCACCCCTCTGCTCCCCCAATGGCTTCATGGGCAACATGAAGCCCTCGGTGCAAAGCAAAAAACCTCGTAAGCCCAGCACTAAAGGCATCGGCTGCAAAGACGGCAAAGATATGAAAGTCAAAAAGAAGAAAGCACAAGACGGAAAGGGAAACTTATTAGACAGCTCGGCTGTTCTCTCTCCGGTGGATTCCCTAGAGTCGCCTCACGGGTATATTTCTGACATCGCCTCGCCACCCCAGATGACATCACCCTTCCAACAATCGCCCTCCATGTCGCTCAATCAGCTACAGGGAATGTCAGACAACCACATGGGCGTCAGCCATCTTGGAATTGGCAACAACCAAGATCTTTCCCATATACAGTTTGATCCATTGCCTCCACGTCTCACTCATCTTCCAGTGGCCGGATCGAACGGTTCAAACGTCATGAACGGCCAATGCGAATGGCTAGGGCGGATGCATGGAAGCATGGCTCCGCAAAACCAGTTCACAGCCATGAGAAACGCCTCAGGTCAAGCCAACCTTCACCAATCAGGCTTGATGACGTCACATCACAATGGCCGCCCTGCCACGCTCTCTCAAATGATGAACTATCAAAGCATGCAGAACACACATCTAATGCAGCAGATGCAGCAGAGCATGCAGCCGCGGCCCCAGCAGACCGGCGTCCAGCTGCAGAGCCAGAGCCAGAACTTCATCGGGGGTGATCTGGGTGGACCGGAGCTCCAGCAGAGCGCAGGGAACAGCATGTCCATCCATACTATAATCCCCCAGGAGACCCAGCTGCTCAACCCGTCCTCTCTGGGGTCCAGCATGGCGGGCACGCAGTTCCTGACGCCACCTTCCCAGCACAGTTACACTCCCGCATTGGACGCCAACACTCCCAACCACCAACTTCAAGTGCCTGACCACCATCCTTTCCTCACGCCATCTCCCGGTTCTCCAGACCAGTGGTCCAGCTCGTCACCCAATTCCAACATGTCCGATTGGTCGGAGGGTATTTCCAGTCCTCCCACCAGCATGCAGTCACAAATCGGACACATGCCCGAGCAATTCAAGTAGAACAATGAGATTCGCTAAATGAAGGCACATTCCATAAGCCTGCTTATACTGAAGGGTCTTTTATACGCCGCTTGTACTAACCTTTTTTTTTCTTTAATTTATTGACATTTTGTTATTTATATACTTGTCATCATTTTTTTTTTAATTTGGGCACAAAACATTAAATCTTAAAGTCGGCATGAAATGAAACTTAAAATTGTTGATTTTTCACCTAACATTACATCCGATTGAAACGATTTGTGAAATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.212 A=NA C2=0.848
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(34.4=100)
A:
NA
C2:
PF127962=Ank_2=PD(32.3=7.0),PF119363=DUF3454=WD(100=15.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCAGCGATGGTGTTGCTTA
R:
GTGCTGGGCTTACGAGGTTTT
Band lengths:
358-1789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]