RnoINT0131952 @ rn6
Intron Retention
Gene
ENSRNOG00000000500 | Scube3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:RGD Symbol;Acc:1304880]
Coordinates
chr20:7737784-7738716:+
Coord C1 exon
chr20:7737784-7737900
Coord A exon
chr20:7737901-7738590
Coord C2 exon
chr20:7738591-7738716
Length
690 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGC
5' ss Score
7.79
3' ss Seq
TTTTCTGACTCCTCCCACAGATG
3' ss Score
11.58
Exon sequences
Seq C1 exon
ATATAGATGAGTGTTCCTTTGATCGAACCTGTGACCACATGTGTGTCAACACTCCGGGAAGCTTCCAGTGTCTCTGTCATCGAGGCTACCTTCTGTATGGCATCTCTCATTGTGGGG
Seq A exon
GTAAGCCAGCAAGCTCACACCCCTGCTTCCAAGCTGCCCCAGCTCCTCGCCCCTTCACATCCCAAATGTCTGATGTTCCCATGCTGGCTTGTAATGAGAAACCACTGGGTGCATGTGTCATGTGTCATCCAACGTGTAAAACAGAAGGCAGCTTCCAAAGGGCAGCTGGGAGACAGGGTACCAGAGAGTAGCATCCTGGCAGCGAGATGTTTGTTTGAGGGTTTCACGGAGCCCAGGATGGCCTCGACACACGTGTAGTCAGAGGTGACTCTGAACCCGATCCTCCTGCCTTCACTTCTCAAGGGTTGCGGCTACAGGTGGCACACTCCCATGCCTAACTCTACCCTGCATTCCCTTGGCTGTGCCCAGAGACCGCCCTCAGTCTGTGGCTCAGTGAGAGGGAAAGAGAGGAAGGCTCTGAAACCTTCATCTGGTTGGACTGGCCCCTGCTCAACAGCGACTTTGACTGTAGAGAAGGGAAAGAAGTTTGAGCTCTTCGCAGCCCAGAGAACCGTCTCATATATTTGCGAGAATGTTTAACGTGAGACCTACCTACCAGACAGATTTGTAAATACATAGTCGTCTCTATAAGGTAGTCAGTTACCATGCTTAGCTCAGCTCCTCCCTCGAAGCCCAGTCCCTGGCTCTTATGCCTGCACCACTGGCAGTGTTTTCTGACTCCTCCCACAG
Seq C2 exon
ATGTGGATGAATGCAGCATCAATAAGGGGGGCTGCCGCTTTGGCTGCATCAACACCCCAGGCAGCTATCAGTGTACCTGCCCGGCAGGCCAGGGCCGCCTCCACTGGAACGGAAAGGATTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000500:ENSRNOT00000000593:9
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:
PF0764510=EGF_CA=WD(100=95.0)
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:
AGATGAGTGTTCCTTTGATCGAACC
R:
TGTGCAATCCTTTCCGTTCCA
Band lengths:
238-928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]