RnoINT0143958 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78110474-78110842:+
Coord C1 exon
chr4:78110474-78110520
Coord A exon
chr4:78110521-78110671
Coord C2 exon
chr4:78110672-78110842
Length
151 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
CTGCCCCTTCACCCTGGCAGTGG
3' ss Score
6.82
Exon sequences
Seq C1 exon
CACCTGCAGCTCTGGAGAAATGGTGTGCACCTCAGAGCGCTGTCCAG
Seq A exon
GTACTCCCTTCATGTGGTGGTCGGTGCTGAGACTATGGGAGACTTTAGACCCTTCAGAGATAGCCTCCTAGGGTGTGGGTAATGTCCCTGGAAAGTCCGGGTCCAGGACAGTTCAGCCTGGTCTCAGACATCTGCCCCTTCACCCTGGCAG
Seq C2 exon
TGGCCTGTGGCTGGAGCCCCTGGACTCCATGGAGTCCTTGCAGCCAAAGCTGTAATGTGGGCATTCGACGGCGCTTCAGAGCAGGCACCGCACCGCCCGCTGCCTTTGGGGGTGCCGAATGCCGAGGTCCCAACCTAGATGCTGAATTCTGCACTTTGAGGCCATGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:58
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:
PF053758=Pacifastin_I=FE(53.3=100)
A:
NA
C2:
PF053758=Pacifastin_I=PD(3.3=1.7),PF0009014=TSP_1=WD(100=87.9)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAGCTCTGGAGAAATGGTG
R:
GCATGGCCTCAAAGTGCAGAA
Band lengths:
210-361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]