DreINT0131745 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8907332-8909061:-
Coord C1 exon
chr4:8908864-8909061
Coord A exon
chr4:8907485-8908863
Coord C2 exon
chr4:8907332-8907484
Length
1379 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGG
5' ss Score
5.61
3' ss Seq
TCTTTTCTCTCTTTTTTTAGCCC
3' ss Score
11.16
Exon sequences
Seq C1 exon
ATCAGATATGTGGTGGAGAGCTGGGCGACTTCATGGGCTACATCGAATCTCCGAACTATCCCGGTGACTATCCATCTAATGTGGACTGCGTCTGGACCATTAACCCTCCAAACAAAAGGCGGATCCTTATTGTTGTACCAGAGATCTTCCTCCCCATCGAGGATGAGTGCGGGGATGTTCTCGTCATGAGGAAGAGTG
Seq A exon
GTATGGTATATCTTTATGACAAGCTTTTTTTTTTTACATTTCACATAATTTCATGCTATTAGTATTAGTACTTTTTAACTTCTTCTAATATCTTTTACATTAAATGGTAGGAGTTATTTATTAGCTACTTGTGTGTCTTGGATAATAGTGTTTATGCTTAAGATATTTTAAAAGATACTAGTCCTTCTTTATGTTTTTGAAAATTTTTTTTTAGATTTTACTATTAAAATTTTAATCAAACTCTACTGTGACCATTCTGACTAATCATAACATAAAATGATTTTTAAAAAGTAACTAGTGACTAGTAAGATATAAATGTTTACTAATAAATAATAAAAACATACCAGATCTAGATGCATATGAACTACTATCTGATAATAAAGAATTACTATGTAATAAATAAGTGCATGTACCTTTAAAAAAGTATTAGTACATAATCAATGAGCAAGAATAACTACTAATAAGTGCTATTATTTACAGGAAATGATGCTTGAAAATAGGCATTAGTGCATTTTTATAAAGACTGTCGTTTTGGATGTTAGTTAAGCACACTACCTAACAGAAATCTTGTCGACTATCCAAGTTTTCGAAAAAACAAATAATAACTTGACTTCTAGTTAATCATTTGGTATCATAAGTGGCTTATCTGAAAGGCAAATGCCTCTAGATTATGCTTATTTCACCAAAATAAAATATGATCATGCCTTGATTTTTTATTATTTAATTAGATGTAGGAACCTCTGCAATGACTCAAATAACTTATTAATAAAGTCATCTGGAATGGAAAAGAAAGCGTTCTTGCAGGACTCCCAGAGTTCATTAAGACTCTTTTTGATCTTCAATGCCTCCTCCATCTTACCCCAGACATGCTCAATAATGTTTATATCTGATGCCTGGGCTGCCAATCCTGGAGCACCATGACCTTCTTTGCTTTCAGGAACTTTGATGTAGAGCCTGAAGTATGAGAAGGAGCGCTATCCTGCTGAAGAATTTGCCCTCTCCTGTGGTTTGTAATGTGATGGGCAGCACAAATGTCTTGATACCTCAGGCTCTTGATGTTGCCATCCACTCTGTAGATCTCTTGCACGCCCCCATACTAAATGTAACCCCAAACCATGATTTTTCCTTTACCAAACTTGACAGATTTCTTTGAAAATCTTGGGTCCATGCGGGTTCCAGTAGGTCTTCTGCAGTATTTATGATGATTGGGATGCAGTTCAACAGATGATTCATCTGAAAAGTCTACCTTCTGCAACTTTTCCAAATGATCAACTAGAATATTCAAGTTATTATTTGTTCTTGGGATCAAGACGAGACTCAGGTAGTGTATTGCTGCAGAAATGCATGTTATTAAGCTACTCTTTTCTCTCTTTTTTTAG
Seq C2 exon
CCCTGCCCACTTCCATTACAACTTATGAGACCTGCCAAACTTATGAGCGACCGATCGCCTTCACCTCCCGTTCACGCAAACTGTGGATCCAGTTTAAATCCAATGAGGGTAACAGTGGAAAGGGATTTCAGGTTCCATATGTCACTTATGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:20
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:
PF0043115=CUB=PU(56.4=92.5)
A:
NA
C2:
PF0043115=CUB=PD(42.7=90.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGATATGTGGTGGAGAGCTGG
R:
AGTGACATATGGAACCTGAAATCCC
Band lengths:
342-1721
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]