DreINT0105461 @ danRer10
Intron Retention
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65004868-65006874:-
Coord C1 exon
chr5:65006576-65006874
Coord A exon
chr5:65005016-65006575
Coord C2 exon
chr5:65004868-65005015
Length
1560 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AACCATTGTTTCTCATGCAGATT
3' ss Score
8.44
Exon sequences
Seq C1 exon
ATGGCTTTACTCCTCTGATGATTGCGTCCTGCAGTGGAGGAGGGCTCGAAACGGGAAATAGCGAGGAAGAGGAAGACGCTTCAGCAAACGTCATCAATGATTTCATCTATCAGGGCGCCAACCTTCACAACCAGACAGACCGCACGGGTGAGACGGCTCTACACCTGGCTGCCCGCTACGCCCGCTCAGACGCCGCGAAACGACTGCTGGAGGCCAGTGCTGATGCTAACATCCAGGACAATATGGGCAGGACTCCATTACATGCCGCTGTGGCTGCTGATGCCCAAGGCGTCTTCCAG
Seq A exon
GTATGTGGAACAATATACAGTCGGGGAAATAAGTATTGAACACATCACCATTTTTCTCAGAAAACATATTCCTAAAGGGGCTGTTGACTTGAAATTTCACCAGATGTTGGCCAATACGGAAGTTACTGAAACTGCAATTCATCGAAATTCCGCTAGTCCTGGCTCCATAATAGAGCAAATTTCAATTGAGCCCACTGTTAGAATGGCCAACTTTATAGCAAAAAAAAAGGAGTTTAAAGCCGGGTACAAAGAAAGATTTTGGTTAATACAGCTAATATTACCCTTCATGACAACTGTGAGGGGGGTGAATTTTTTTATAACTCATCAGTTTCCTTTATATTAGGTTATATTAAGTTTGCATAATTAAGGGCGTGGCCACTTGAGTGACAGCTAGGTCTCGTTGGTCGCCGTCACGTCACCTCAGCTGAATCCTGCAGATTAGCCACTGAACTCGGCATATTTATCGTATTTCTGTGTTGTTTTATGTGGCTTTACACAGTCAACTGCCTTTTGGGATTATTTCCTACAATTATCAGATGGCATGCTGAGTGCACTTAATTGTGCTCACAAACCATTCACGTGACCTCCGTTTCCCATGTGAGTAAAGTTATATAGTGTCTGTAGCTCCGCTCACTCTCCGCCTCTTTGCCCTTGTTTGGCCGCGCCTACTTGTGGCTTCTTTTGATCTCTTCAGAAACCTATGGGTGACATCACGGACACTACGTCCCTATATTTTACAGTCTATGGTAACAACCAAAGAAATCCATATATGCAAAGAAAACGAATCTAATTAGTTTACAAATGAAGTTATGTGTAATAAAATGAAATGACGCAGGGAAAAACTAGTGGATACATGAAGAAAGGGAGGTGTAGAAAGGCAGTGAAAGCCCAGACAGCAGCTGAAATCTCTCAGTAGTTCTTCAGCAACCCTCTGCTCTTCGTCAGTGTGAATGAATATTAGCTGCTTCAGTCCAACATCTACATTAGGAGGAAGGTGAATCCAGGGTGGACATTTCAGCAAGACAATGAGCCAAAACACAGCCGAGGAAACTCTCAGATGTTATCAGAGAAAGAAAATGAAGCTGTGGAATGGCCAAGCCAATCACCTGACTTGAATCCGATTGAAAATCTAAAATAAAGCTCTGATTTGATAGATAAGACCCACAGAAGTATCGAGATTTCTACATTCTGTTGAAGTCTTTGAAAAACTCACAACTGAACAATGCATGTGACTTCATTCTCCATATAAGAAGCGTCTTTAAGCTGCCATCACCAAAAAAAAACCTTTTATATAAAGTATTAAATACATTTCAGTACTTTCTCCTTGTGTCATTCCATTCTTATTACACATAACTCATATTTCAGATTTTTATATTTGTATAGTTTATCTATTTACCAAAATCTGGTTCAATTTAACCCCAACAGCTCCTTTAGAAATATTACTCTCAGGAGAAAACATGCCGTGTTCAATACGTATTACCCTCACTGTAATGCGGTTGATGGAAATGATATTGCTTGTGTCTGTTTTCCTAAAGATGTTAACCATTGTTTCTCATGCAG
Seq C2 exon
ATTTTGATACGGAACCGCGCCACAGATCTAGACGCCCGCATGCATGATGGCACCACACCTCTGATACTGGCCGCAAGACTGGCGGTCGAGGGCATGGTGGAGGAACTCATCAACTGCCATGCTGACGTTAATGCCATTGATGACTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094:ENSDART00000130888:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(83.3=75.0)
A:
NA
C2:
PF127962=Ank_2=PD(14.4=26.0),PF127962=Ank_2=PU(31.2=58.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGACGCTTCAGCAAACGTCA
R:
AACGTCAGCATGGCAGTTGAT
Band lengths:
356-1916
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]