RnoINT0143995 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78126856-78127267:+
Coord C1 exon
chr4:78126856-78127014
Coord A exon
chr4:78127015-78127150
Coord C2 exon
chr4:78127151-78127267
Length
136 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATC
5' ss Score
6.99
3' ss Seq
CTTTTACTTCTGGATCCCAGGTG
3' ss Score
7.08
Exon sequences
Seq C1 exon
ACACATGCCAGTGGGGACCTTGGGGACCTTGGAGCCCCTGCCAAGTGCCCTGCAGTGGAGGATTCAAGCTACGCTGGAGAGAGGCAAGCGACAACTCTGTGGGAGAATGCCGTGGACCATGGGCTCAAACAGAAAGCTGCAATATGGGATCTTGCCCAG
Seq A exon
GTAATCAGTATCCCAGCATCCCAAGGGTATGGAGATTGGTGCCTCTGCCCTGGTGGTTTATAGTGGAAGAGAGGGTCTGCTGGGGATGGGGTGGGCAAGAGTGCCCCCAGTATACACTTTTACTTCTGGATCCCAG
Seq C2 exon
GTGAGAGCTGTGAGACCAGGGACACTGTGTTTACCCTGGACTGTGCCAACCAATGTCCTCGCAGCTGTGCTGACCTCTGGGAAGGTGTTCAGTGTCTACAGGGACCCTGCAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:91
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=WD(100=87.0)
A:
NA
C2:
PF0182612=TIL=PU(63.2=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACATGCCAGTGGGGAC
R:
ACTGAACACCTTCCCAGAGGT
Band lengths:
252-388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]