RnoINT0131941 @ rn6
Intron Retention
Gene
ENSRNOG00000000500 | Scube3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:RGD Symbol;Acc:1304880]
Coordinates
chr20:7741825-7742491:+
Coord C1 exon
chr20:7741825-7741986
Coord A exon
chr20:7741987-7742293
Coord C2 exon
chr20:7742294-7742491
Length
307 bp
Sequences
Splice sites
5' ss Seq
AGAGTACGC
5' ss Score
3.97
3' ss Seq
CCACTGGGCTATGGCTGCAGATA
3' ss Score
5.18
Exon sequences
Seq C1 exon
TCCAGTGCTCCCCGGGCCACTACTACAACACTAGCATCCATCGCTGTATCCGCTGTGCTGTGGGCTCCTACCAGCCAGACTTCCGCCAGAACTTCTGCACCCGCTGCCCAGGAAATACAAGCACGGACTTCGATGGCTCTACCAGTGTGGCCCAGTGCAAGA
Seq A exon
GTACGCGGCCAGCGAGGCTGTGGGAAGTGGGGAGAGATCTTGGAACCATGTGCATGGAAAGGGGGGTGGTGGTAAAGCAGCAGAAGCAGGGTTGATGAGTGGGTGGGCCGCGGCCAGCTGTCAGGGTGAGGCCGGTAGCATCTTTTTAGATACCGGATGGGCAAGGAGGAGGGTGGACCCAGAACCCCGAAGAGCATGGTCCACCATCCGCATCCATCCTCCACCTTCCAGCTCTTCAGCCTGCTCAGCGTGGCTCCCCACTGACTCTCATCTCTCTCTTGCTCTCCCCACTGGGCTATGGCTGCAG
Seq C2 exon
ATAGGCAGTGTGGCGGGGAGCTGGGTGAGTTCACTGGCTACATCGAGTCTCCCAACTACCCGGGTAACTACCCAGCTGGTGTGGAGTGCATCTGGAACATCAACCCCCCACCCAAGCGCAAGATCCTCATTGTGGTCCCTGAAATCTTCCTGCCGTCCGAGGACGAGTGTGGGGACGTCCTGGTCATGAGAAAGAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000500:ENSRNOT00000000593:18
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:
PF076998=GCC2_GCC3=WD(100=87.3)
A:
NA
C2:
PF0043115=CUB=PU(57.3=94.0)
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:
CCGGGCCACTACTACAACACT
R:
TTCTCATGACCAGGACGTCCC
Band lengths:
343-650
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]