RnoINT0131947 @ rn6
Intron Retention
Gene
ENSRNOG00000000500 | Scube3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:RGD Symbol;Acc:1304880]
Coordinates
chr20:7730836-7731848:+
Coord C1 exon
chr20:7730836-7730970
Coord A exon
chr20:7730971-7731722
Coord C2 exon
chr20:7731723-7731848
Length
752 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGC
5' ss Score
7.09
3' ss Seq
AGCCTCTCCTCCCTTTTTAGAAG
3' ss Score
8.79
Exon sequences
Seq C1 exon
ACGTGGATGAGTGTGCAGAGGGCAATGGGGGCTGCCAGCAGAGCTGTGTCAACATGATGGGCAGCTATGAATGCCACTGCCGAGATGGCTTCTTCCTCAGTGACAACCAGCACACCTGTATCCAGCGGCCAGAAG
Seq A exon
GTCAGCCCAGGGCCTTTGCCTGAGGTCCCCAGGCTTCTCTTCCCCACCTTCCTTCCCTCAGCACTCCCCGTCCCACACTCTAGGTTCCTCCCCTCTACCCTTTCTCTGACTCACAGCCTGAGGGTTTCATGTTAGACACAGAGACAAGTCTGCAGAATGGACAGAAGCTACCTTGGGGCATTCTCTGGTCCAGCTGCAAGGTGAAGCAAGTTTCTGTTGGTGAGCATTTGTCTGTAAGCTGCTACTTCTCTGAGACAGCCTCACCTGTGTCCCCTTCCATGATCAATGGCTCATTCCCTCATCGGATTTTGATATTCTGAGAGCAGCAGCTGGGTTTAATTTGCCTTTGTGTCCTTGTCACCTAGCATGCCACCTTGCCTATGGCAGAAGCTTAATAAAATGTGTGGTCTAGGCAGGTGTGGTGGCTCACACCTTTAATCCCAGCACATGGTAGACAAAGGCAGGCAGATCTGTGAGTTCAAGGCCAGCCTGGTCTGGAGGGTGAGTTGCAGTACAGCCTGGCTACAGAGAAACCCTCAGTCTGATGGCTGTTTTATCTTCTAATGCTTTCTTGTCTCAGTGTGCACTTGGAGGGAAGAGATCCTGTTTTAGTTTTTCTGGGCCCTTCCTAGATGCTGAGAACCTCTGAGTAGCAGGCTTGGTTGGTCCTTATGAGCGTCCTTAGCCACAATGGTTCACCCCACTGAGGCCTCCGGGTGCAGATGGAGCGTCAGCCTCTCCTCCCTTTTTAG
Seq C2 exon
AAGGAATGAACTGCATGAACAAGAACCACGGCTGTGCCCACATTTGCCGGGAGACTCCGAAGGGGGGCATTGCCTGTGAATGCCGCCCTGGCTTCGAGCTCACCAAGAACCAACGGGACTGTAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000500:ENSRNOT00000000593:4
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:
PF126622=cEGF=PD(12.5=6.5),PF146701=FXa_inhibition=WD(100=78.3)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=86.0)
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:
ACGTGGATGAGTGTGCAGAGG
R:
GTCCCGTTGGTTCTTGGTGAG
Band lengths:
254-1006
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]