RnoINT0131890 @ rn6
Intron Retention
Gene
ENSRNOG00000010617 | Scube1
Description
signal peptide, CUB domain and EGF like domain containing 1 [Source:RGD Symbol;Acc:1309015]
Coordinates
chr7:124523860-124525356:-
Coord C1 exon
chr7:124525240-124525356
Coord A exon
chr7:124523983-124525239
Coord C2 exon
chr7:124523860-124523982
Length
1257 bp
Sequences
Splice sites
5' ss Seq
GAGGTCTGC
5' ss Score
3.9
3' ss Seq
TCTCCTGCCTGTGTTTCCAGACG
3' ss Score
9.45
Exon sequences
Seq C1 exon
ACATTGACGAGTGTTCCTTTGAGCGGACCTGTGACCACATCTGCATCAACTCCCCCGGCAGCTTCCAGTGCCTGTGTCACCGAGGCTACATACTCTACGGGACAACCCACTGCGGAG
Seq A exon
GTCTGCAGCCCGTCTGCCAGGGCCACCTCCCCCTCGAGGCACGCGCCTGGCAATGGCCATCCATCAACAGTGCTCCCCACACCCCAATCCTGACCTTGACTCTGGTGGGCCTGGGAGGGACCTTGCAAGGCTGGGATTCTGACAAACAGGCACGAGGTAGACAACGGGGGCTGGGGGCAGGCAGGGCCTGGGAAGCACCATGAGGGTGCCTTAGACAGCTTGGAAGCATAAGCCCAGAACCTCATTTCCTGGGGTGCCCAGTCCAGAAGTGGGTGGCCAATGCACAGAAAATTCCAAAATGTGCATTCTGGAGACAGGAAGGATGGTGAGACAGTAAGAATCCTAAAGGAGGAATGTTTGGGGGCCAGCACTTACAGACGCACAGAGGCAAGGATGTAGCAGGGCATCGGGAGCATCAGGAAACAGGGTAATATCCCCCAGGGAGATACGCGCCCAGGATATACAGAGCGGTAGGAGCCTGGAGAAAGCTCTAGGGCTTCTTTACAGTGCTTCACACCGAAGCAGGAAGCCAAGATAGTCATATGTGTGTGACAACGGACTCTGGCTTTTGGAGGAAGGGAGCATGAGATCCAGGCAGCCCACGGGGGAGATGTCTCAGGGCCTGAGACCTTAACCTCTGGGGTAAGGGGTGGGGGTGGGAGGGCAGAGCTGGACAGAAGATTCAGGAGCCTGGGAGGGAGGAGTTCTTACTTAGAGCCCTGGATCCCATGGCCAACACCACAGTGAACAGGAGCTTGAGCTGAGCCAAAGGACATTAGGCCAGATGTGGCTGGTGAAGATGGGCGGGGTGGGGTGCGGGTCATCGTGACCTCTCTTCTTTCTCTGTGGCCTGAGAACTAGAGAGGGCCAGGCAATACTGGAGCCACTAGATACTGGTGCCACTGTCAAGGGACTCTCAAACACCCCTTCCCTGACTGATGGGATGGGACATTTGTGTGCTGGCAGCCCAGGTGGCCTGGAGCAGGAAGAGCTAGCTGGCCCTTGCTCAAAGGGGGCTTTTGGTCAGAGGAGGAAGAGTCTCAGGTGACTTCTTCCAGGCCTGATACCTATTATCCAGTGGGTAAACTAAGGCTGGCAAGGAGCCGCTGCTTTCCCTGAGGGGATGAGACATCCATGGTGCCAGGACCTCTGCCAGTCTGGACTGGGATCATGAGCTTCCTGGTCTCTGGTCCTGGGTGTGGCCTGTCCGGTGGTTCCCACCCATTCCTGCCCTCACTCTCCTGCCTGTGTTTCCAG
Seq C2 exon
ACGTGGATGAGTGCAGCATGAACAACGGCAGCTGTGATCAGGGCTGCGTCAACACCAAGGGCAGCTACGAGTGTGTGTGCCCACCAGGGAGGAGGCTGCACTGGAATCGGAAGGACTGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010617:ENSRNOT00000017727:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=95.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTGACGAGTGTTCCTTTGAGC
R:
CCACACAGTCCTTCCGATTCC
Band lengths:
239-1496
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]