RnoINT0143986 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78123528-78123801:+
Coord C1 exon
chr4:78123528-78123680
Coord A exon
chr4:78123681-78123754
Coord C2 exon
chr4:78123755-78123801
Length
74 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
GAATCGAAGCTCTTTTCTAGTTC
3' ss Score
-0.71
Exon sequences
Seq C1 exon
GTCCTCCACATCAGGCTCATGGGCCCTGGAGTGTCAGAAGGAGCAGTCACAGAGCCAGCCGTGCCCTGAGGACCCCTGCCCACCCCTGTGCCTACATGAAGCCCACCTTCATGTTCTGGGGGACAACTGGCTGCATGGAGAATGCCAGCAGTG
Seq A exon
GTAAGTACAGTCCAGGAAAGGGTGACCCACTGTCCTGCTCGACAGCAAGACCCTGAATCGAAGCTCTTTTCTAG
Seq C2 exon
TTCCTGCACCCCAGAGGGAGTCATCTGCAAAGACACCGACTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:83
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:
PF0009014=TSP_1=PD(53.1=50.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGTGTCAGAAGGAGCAGT
R:
CACAGTCGGTGTCTTTGCAGA
Band lengths:
171-245
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]