DreINT0105451 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65023750-65025906:-
Coord C1 exon
chr5:65025774-65025906
Coord A exon
chr5:65023999-65025773
Coord C2 exon
chr5:65023750-65023998
Length
1775 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGA
5' ss Score
6.8
3' ss Seq
TTTCTTATACTTTTTTCCAGGTG
3' ss Score
10.94
Exon sequences
Seq C1 exon
TGTGTGCCAGGTTATCATGGAGTGAACTGCTCTGATGAGATCAATGAGTGTCTGTCTCAGCCCTGCCAGAACGGGGGCACATGCATCGACCTGATCAATACCTACAAATGCTCCTGTCCTCGGGGAACACAAG
Seq A exon
GTCAGATTTCACTTCCTCCTCTGTTTGGCACTTTTTCATGCTTCGTTTTCTTTATTAATTACAGCTTGCACATTGACTGATGCTTTCATGCTTAATTATGGAACCGCTTGATTGTTTTATGTTCAATCCACTTAAATTTGTAAAAAGAATTACGTTTTAATTGAATCTTTTTGTGTTAGGACGAGTGTTGTGCTAGTTACTGAAAAATAGTAACTAGTTACAGTTACTATGAGTAACTCAGTTACTTTATTGATTACTTACACCAAAAAGTAATGAATTATTATAAACAGTCATACATTTTATGCATTTTAAACAAAACAAAAACGTAACAGCTGCTTAAAACTGAAATCTATCAGCAGTTTTTAAACTAACCACAAATTAAACGTGGTATGTCAGCAACTTATGGAAAGTAAGCTGTGTACATTCAAAGTGCAAAATCTGCTGTTGTATAACGGCTATAAAAATATGTAAAACAATAAACAAATGTTAAAAAATCAGTATTTTTCTGATCAATACAACACTATACATTTAAACAATGTGTTTAGAAATATGACAGAAATGTGTCACTGTGTCTACTAAACTAATCAGTTGTGTTATACAGAAAACAAAAGTGTGCTTATTTATTTGAAGCAACAAACATAGTAGCCCTGGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTGTCTGTGTGTGTGTGCGCGTGCTGTATTTATAGTCCGCGTAATGAATGAATGATGAGCTTCAGCTGTGTCTGTGTGAAATCATCTGATCTCGGAAAAGGTGCATGTGAGCGGTGCATGACTGGACCTTGTAGTCCATGTAATGACGGATTTGTAGTTCATTGCGATCTGTGTGTTAACCAGCAATCTGCCAGGATTAGATCGCTGGTGATTGTGAAAATTTATAATAATAATTACGTTTTAATTGAATCTTTTTATGTTAAGACGAGTGTTGTGCTAGTTACTGAAAAATAGTAACTAGTTACTAGTAACTAGTAGATTTATAATAATAATGATAGTAGTAACCTTATTAGCTTCTTAGTTTCTCATGCGCACGCATTCGGTCTCTTTCACAAACACACTTGGCCTCTCTTGCGCGCACCTGGTCTCTCTTGTGCACACCCAATCTCTTGTGCGTGCTCGGTCTCTCTTGCGCACACACTTGGTGTACCTTGCGCGCATTCAGTCTCTGTTTCTGTGTGACTTTTGTGAAATCTCCTCATACACAACGTGTTTTCTTTATGGTAATTGGTTGGCATCAACCAATCCCACAATGCGATGCCGCTGTAAAAAAAGAAGATGTGGGCTAGACTGCAGCCAAAATAATTAACTTACCAAGTAACGGACAAACACATCATAACGATAACGGAGTTATTTATTTAAAAATTAATGCGCTACAATATTAGTTACTGTCAAAAGTAATGCCATTACAGTAATGCATTGTTAGAAACGCGTTATTGCCCAACACTGGTTAAGGCAACATGCAGTAATTTTGTGTTACCCAGCATTTATTTTCTAGTGTAGCTAGAATGTACACTGTAAAAAATACTGGGTTCTACACAAGTGCTTTGTGTTGGGACAACATAAAGAAATTAAGTTAATTATTAGTTTTTACAAATTTAAGTGGATTGAACATAAAACAGTTAAGTTGTCCCCAAAAAAATCTCAAGAGTTGTGTTGTTTCAGCTCATTTTAAATTAGTAGCTAGAACAAGCAACAAAAAAAAATGTTATTGAGTATATAAGTGCAGCTTTTCTTATACTTTTTTCCAG
Seq C2 exon
GTGTGCACTGCGAGATCAACATTGACGACTGCACACCGTTCACTGACCCCATCACCCATGAGCCTAAATGCTTTAACCAGGGCCGCTGTGTGGACCGTGTGGGCGGCTACCACTGCATCTGTCCCCCTGGGTATGTTGGGGAACGCTGTGAGGGCGACGTCAACGAGTGCCTGTCCAACCCCTGTGGCACACACAGCTGCATCCAGCTCAAAAACAACTACCGCTGCGAGTGTCGCACAGGATACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:22
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(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
A:
NA
C2:
PF0000822=EGF=PD(6.5=2.4),PF0000822=EGF=WD(100=46.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGTGAACTGCTCTGATGAGA
R:
ACTCGCAGCGGTAGTTGTTTT
Band lengths:
347-2122
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]