RnoINT0131902 @ rn6
Intron Retention
Gene
ENSRNOG00000010617 | Scube1
Description
signal peptide, CUB domain and EGF like domain containing 1 [Source:RGD Symbol;Acc:1309015]
Coordinates
chr7:124503968-124504622:-
Coord C1 exon
chr7:124504470-124504622
Coord A exon
chr7:124504048-124504469
Coord C2 exon
chr7:124503968-124504047
Length
422 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
CCCTGCTGGCCGGCTCCCAGAGG
3' ss Score
5
Exon sequences
Seq C1 exon
CCTCGCCCACGTCAGTCACCACCTATGAGACGTGCCAGACCTACGAGCGGCCTATCGCCTTCACCTCCCGCTCCCGCAAACTCTGGATCCAGTTCAAATCCAACGAGGCCAACAGTGGCAAAGGGTTTCAAGTGCCCTACGTCACCTATGACG
Seq A exon
GTAAGACACCACCATCTCATCACAGCCCACTCTGTGTCAGCCAAGGCCTGGCTTGGGAACTCAGAAATGAGTTGCACATCCTGCCTCTGACAAACCAGAGACAGGACTGAGGGCTAGGCAATGTGGAAACCCAAGGGGTATAAGGGTATATATAGGCGAGAAGAGGGGGACCGTGGGTACTCTCTGTGGGCTTCACAGAAGGTCCCACCCCACCAGGGCTTGCAAGGTTAAATAGGGGCAGCAAAGCCACCAGGAGGACAAAGCAGGTGGAGGGGACCCCAGAGCAAAGGCCAAGAGACACAGCTCCAGCCAGCCACCACCAGCTGTCCAAGGCGGGTCCAGGGAGCTGGGGAGGGCAGAGGAGGGAGGTGTAAGGTCTCAAGCCCCCTCCACCTTCCCTCTCCCTGCTGGCCGGCTCCCAG
Seq C2 exon
AGGACTACCAGCAGCTAATAGAAGACATCGTGCGCGATGGGCGCTTGTATGCCTCGGAGAACCATCAGGAGATTTTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010617:ENSRNOT00000017727:21
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=PD(41.8=88.5)
A:
NA
C2:
NO
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:
CTCGCCCACGTCAGTCAC
R:
TCAAAATCTCCTGATGGTTCTCCG
Band lengths:
230-652
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]