DreINT0131739 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8911906-8913926:-
Coord C1 exon
chr4:8913768-8913926
Coord A exon
chr4:8912113-8913767
Coord C2 exon
chr4:8911906-8912112
Length
1655 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
TTCTTTTATTTATGTTTAAGAAT
3' ss Score
6.62
Exon sequences
Seq C1 exon
CTGGCCAGTTCCCTTGCACAGACGACTGTCAGGTAACATTTGTGAATCTGAAGTGCGACTCTTCCAAAAAGCGCCGTAGGGGCCGGAAATCTCCCTCAAAGGAAGTCTCGCACATTACAGCAGAGTTTGAGATGGAAATGAAAGAAGAAGAAGCCTCAG
Seq A exon
GTAACATTGCCTGCATATGTTTAAATAATTATTTAATACATTGCAAATGTAGGATTTGGGTGTTTTTACATAGCTCTCAAAAGTCTTTAATTTCACTTACACAACGTTTCGACCAACATGGTCTTCATCAGGTCTCACACAAGGTTTCGACCGACATGGTCTTCATCAGGTGTGGCCTGTAATTTTCATCATAGGTACACCTCAACTATTAGAGACGAAATCAGAAAAAAATCCAGAAAATCACATTGTAGGATTTTTTAAAAAATTATTTGCAAATTTCCGTGGAAAAATAAGTATTTGGTCAATACCTAAATTTAATCTCAATACTTTGTTATATACCCTTTGTTGGCAATGGCAGAGGACAACCATTTTCTGTAAATCTTCCCAAGGTTTTCCCACACTGTTGCTGGTATTTTATCTCATTCCTCTATGTAGATCTCCTCTAGAGCAGTGATGTTTTGGGCAACACTGACTTTCAACTCCCTCCAAAGATTTTTAAGGGGGTAAAGATCTGGAGACTGGCTAGACCACTTCAGGACCTTGAAATGCTTCTTACGAATGTTTGGGATCATCGTTATGCTGAAAGACCCAGCCATGTTTCATCTTCAATGATGGAAGGAGGTTTTCACTCAAAATCTCACGACACATGGCCCCATTCATTTTTCCCTTTACACGAATCAGCATTCCTGGTCCTTTTGCAGAAAAATAGCCCCAAAGTATGGTTTCCACCCCCATGCTTCAATTAGATATGGTGTTCTTTGGATGCAACTCAACATTCTTTGTCCTCCAAACACAACAAGTTGAGTTTTTACCAGAAAGTTCTATTTTGGTTTTTATCTGACCTTACGCCATTCTCCCAATCCTCTTCTGGATCATTCAAATGCTTTCTAGTAAACTTCAGATGGGCCTTGACATGTACTGGCTTAAGCAGGGGGACATGTCTGGCACTGCGGGATTTGAGTCCCTGGTGGCGCAGTGTGTTGCTGATCTTGAATGAAGCCACAGATCAAAGGAGGTTATCAGTGGTCTTGTATGACTTCCATTTTTTAATAATTGCTCTCACAGTTGATTTCTTTACACCAAGCTTCTTACCTATTGCAGATTCAGTATTGCCTGACTGGTGCAGGTCTACAAATTTGTTTTTGGTGTTCTTTGACAGCTCTTTGGCCATGATGGAGTTTAGATTTTGAGTGTTTGAGGTTGTGGATAGGTGTCTTATAGTGATAATGAGTTCAAACAGATACCATTAATACAGGTAACAAGTGGATTACAGAGAAGCCTCCTAAAGACAATGATGAAGGTTTGTGAGAGGCAGAAATCTTGCTTGTTTTTAGGTGACCAATACTTATTTTACCAAGGAATTTACTAATAGATTCAATAAAACACAATGTGATTTTCTGGATTTTTTTCCACATCTTGTCTCTCATGGTTGAGGTGTACCTATGATGAAAGCTACAGGCCTCGCTGTTACAGCATATGATCTTTGCCTAGAACTAGTTCATATATATATATATATTTTTAGCATTATTATTACAATCCCACTGTTACCGGAAAAGATATTATATTAAATATTATATTCACTATTGTGCAAGGCTTTATTTAATCTGACTTGCCTGCAGCGTTAAGTTCTAACATTTCTTTTATTTATGTTTAAG
Seq C2 exon
AATCATGCAACTTGGACTGCGTTCGCGAGAAAACCAAACAGCGATTACAGAACGCCATGCGCACACTAAGAAAGTCCATCAGTAAGCAACAGTTCTACATCCAGTTTTCTGGCACCGCATATGAAGTTGCCCAGCATGCTTTACGACATACGACTGAAGGAGATGAAACCTGCAGTATAGGACAGGTCTTTACCGATGGGAAGTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.426 A=NA C2=0.071
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTTCCCTTGCACAGACGAC
R:
CCCATCGGTAAAGACCTGTCC
Band lengths:
354-2009
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]