RnoINT0143904 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78131239-78131693:+
Coord C1 exon
chr4:78131239-78131299
Coord A exon
chr4:78131300-78131562
Coord C2 exon
chr4:78131563-78131693
Length
263 bp
Sequences
Splice sites
5' ss Seq
TGGGTACAG
5' ss Score
0.89
3' ss Seq
TGCTACTCTCTTACCTCCAGAGG
3' ss Score
8.67
Exon sequences
Seq C1 exon
GGTGAAGTGGTCGTGCAGGAGCCAGGGAGCTGTTGTCCCATTTGTCAGCAGGACACTCTGG
Seq A exon
GTACAGAGGGTAGGAGAACCTGTATAATGCCTTCCCCTGGTCGGCATCTTTCTGCCTCACAATCTCATGCCCAACCTGCTATGTTCCTGCATTTTCCAGGCTTGCCTGCATGGGGATCATAGTGGCTCCCTCATCCCAGGCCCTGCCCTAAAGTACTCCCCCCTACCCGCAATCCCTGCCCTGCTGCCCACACCTCTCAAGCACACCTCAGTCACTCAGTCATAGCCTCTTCCTCTGTCTTGGTGCTACTCTCTTACCTCCAG
Seq C2 exon
AGGAGGAGCCAGTCTCCTGCAGGCACCTCACAGAACTCAGAAACCTCACCAAGGGTCCCTGTCACCTGGATCAGGTAGAAGTGAGCTACTGCAGTGGACACTGCAGGTCCAGCACCAATGTCATGACTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:100
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:
PF0009313=VWC=PD(25.0=66.7),PF053758=Pacifastin_I=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAAGTGGTCGTGCAGGAG
R:
AGTCATGACATTGGTGCTGGAC
Band lengths:
188-451
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]