RnoINT0143999 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78129017-78129394:+
Coord C1 exon
chr4:78129017-78129144
Coord A exon
chr4:78129145-78129251
Coord C2 exon
chr4:78129252-78129394
Length
107 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ACTGAACCTATCTGCCTCAGCTG
3' ss Score
3.31
Exon sequences
Seq C1 exon
AGTGCCCGCCTGGGCAGGTGCTCAGTACCTGTGCCACTTTGTGCCCCAGCTTCTGCTCCCACTTGTGGCCTGGCACCATCTGTGTGCGGGAACCCTGCCAGCTTGGCTGTGGCTGCCCTGGGGGACAG
Seq A exon
GTGAGTCTGGCCTCTGGTTCTGGTTTCTGTTGGGGAGGGAATGGAAGGAGGTGCAGTTGGAGAGGCATGGGGCCAGGTCCGAGTGTAACTGAACCTATCTGCCTCAG
Seq C2 exon
CTGCTACACAGTGGCACATGCATTCCCCCTGAGGCCTGTCCCTGCACCCGGCTTTCCCTGCCCTGGGGCCTCACCCTACCCTTGGAAGAGCAGGCCCAGGAGCTGCCCTCAGGGACTGTGCTCACCTGGAACTGCACACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:95
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:
PF0182612=TIL=PU(74.5=95.3)
A:
NA
C2:
PF0182612=TIL=PD(21.8=25.0)
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:
AGTACCTGTGCCACTTTGTGC
R:
GTGTGTGCAGTTCCAGGTGAG
Band lengths:
246-353
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]