RnoINT0143959 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78110672-78111326:+
Coord C1 exon
chr4:78110672-78110842
Coord A exon
chr4:78110843-78111194
Coord C2 exon
chr4:78111195-78111326
Length
352 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GACCTGAATGTTACCCATAGGCC
3' ss Score
7.14
Exon sequences
Seq C1 exon
TGGCCTGTGGCTGGAGCCCCTGGACTCCATGGAGTCCTTGCAGCCAAAGCTGTAATGTGGGCATTCGACGGCGCTTCAGAGCAGGCACCGCACCGCCCGCTGCCTTTGGGGGTGCCGAATGCCGAGGTCCCAACCTAGATGCTGAATTCTGCACTTTGAGGCCATGCCAAG
Seq A exon
GTAAGAGTGAGAACCTAGGGTCCAAGACTTCCTTGAAGAACCTATCTAGGGTTCCTTCCAGAGAGAAACCAAGAGTAGCTTTCAGGATCCACGAGTTATAAAAGGGACTTCCCTAAGGGTTCTAAGCAGTGGGTCCCCAGAGGCCTTGCTAGTCTATTTCCTGAGAAAGACCCTCTCTAGAGACCAGTCCACTTCCTCTCTGAAGGCACCAGGTCTCCTAGGACAGAGGTAATACTGCAGGTGAAGTTATACGAGATGAGAAGAAAGAGGTGCCTTTGGACATCTGAGTTTGGGAAGGATGTGTGCTGAGTATGGAAGGTGAGACCCTTAGTGACCTGAATGTTACCCATAG
Seq C2 exon
GCCCTGGTGCAGCATGGAGTTCCTGGACTCCATGCTCAGTGCCCTGTGGTGGTGGCTACCGAAACCGCACTCAAGGCAGTGGCCGGCACAGCCCCGTTGAGTTCTCTACCTGCAGCCTGCAGCCCTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:59
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=0.022
Domain overlap (PFAM):
C1:
PF053758=Pacifastin_I=PD(3.3=1.7),PF0009014=TSP_1=WD(100=87.9)
A:
NA
C2:
PF0009014=TSP_1=WD(100=91.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAGCCCCTGGACTCC
R:
AGGCTGCAGGTAGAGAACTCA
Band lengths:
279-631
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]