RnoINT0131943 @ rn6
Intron Retention
Gene
ENSRNOG00000000500 | Scube3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:RGD Symbol;Acc:1304880]
Coordinates
chr20:7727929-7728789:+
Coord C1 exon
chr20:7727929-7728051
Coord A exon
chr20:7728052-7728663
Coord C2 exon
chr20:7728664-7728789
Length
612 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGTGTGCTTTCTCTGCGCAGACG
3' ss Score
11.32
Exon sequences
Seq C1 exon
ATGTAGATGAGTGTGTGGAGGGCACGGATCACTGTCACATTGATGCCATCTGCCAGAACACCCCACGGTCATACAAGTGCATCTGCAAGTCCGGCTACACGGGGGATGGCAAGCATTGCAAAG
Seq A exon
GTGAGGCTGGGGCGGGGGGTGGCCCAAGAGGAGCCTGCAGGAAAGTGGGGACTAACTCTGATGCCTTGGGAGCTGCACCATGGTTCCCAGAGGCTTGCAGTCTATACAGGCCAAGGAGGACAGCCGCATCTTCCCAGAGATCACGGTGTTCTGGTGGGTACCAGAGCATCGCAGAGCCAAGGTGACGTGCTGGTGGGGACACTTCATAGCCTTGTAGCCACATAGCTGTCTGGGGCTGGCACACCTCAGTTACAAAACTAAGCCTTGAAGAGCCCCGAAACAGGAGCAAATCAAGATCATGCGCAAAGGGCAGGACCAGTTGACCCCAGTGGGAACTCGCCCACGAGCAAGTATAGCTTTTGCTGTAAATGCGCTGCAGAGGAATAGCAGTTCCAAGTGCAATTGAGGCTGCAGGGGACAGAGTGCATGCTACTCTCGGTTGACACAGTACACTGAGAACTGCAACCGCCTCCCGGGACCTGGGGGATACTAGTTAAGTGACGACACTCTTTCCAACTTTATATGAACGGCATAATAAAAAAAAAAAAAGTGAAAGGAAAAGATGGCCTGTTTGCATGGGCCTTCAATGTCCTGTGTGCTTTCTCTGCGCAG
Seq C2 exon
ACGTGGATGAGTGTGAACGGGAGGACAACGCTGGCTGTGTGCACGACTGTGTCAACATCCCTGGTAATTACCGGTGTACCTGCTACGACGGGTTCCACCTGGCACACGACGGACACAACTGTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000500:ENSRNOT00000000593:2
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:
PF129472=EGF_3=WD(100=85.7)
A:
NA
C2:
PF126622=cEGF=PU(83.3=46.5)
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:
ATGTAGATGAGTGTGTGGAGGG
R:
GACAGTTGTGTCCGTCGTGTG
Band lengths:
246-858
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]