RnoINT0144002 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78130286-78131105:+
Coord C1 exon
chr4:78130286-78130494
Coord A exon
chr4:78130495-78131009
Coord C2 exon
chr4:78131010-78131105
Length
515 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
GAGCGTTTCTCCTCCTGCAGCCT
3' ss Score
7.39
Exon sequences
Seq C1 exon
AGTGCCCTCCTGGGGAAATATTGCAGCTTGGGGAGCTGAGGCCTTGCGAGAAGACATGCCTCGAAATGAACAAGACACAGGCTTGGAGCAACTGCACTGAGGCTCAGGTTCCAGGCTGTGTGTGTCAGCTGGGGCACTTCCGCAGCCACACAGGTCTCTGTGTTCCCGAAGACCACTGTGAATGTTGGCACCATGGGAGTCCCCATCTG
Seq A exon
GTGAGACAACAGTCACTTTTCTTGGCCAAGGACTTCCCATCTACTGATCTGTAGCTGTACTGACTCCCTACTTCCAGCCCTGCAGTAGCAGGCAGACTCTGCCTTCTCAGGACCCAGCTGGCCCTAGGTTGAAATCCCCCCTGCTCCTAGCCAGCCTCCAGTCCTGGGCTGTTGCTCTGGCTGAAACTCCCAGGCTGGATTTAGAATTGAGATGGTACCATGGAAATCCCAGGGGACAGCTCAACGAGTAAGGCATGTATTGCTCTTGCAGAGGATCTGAGTTTAGTTCCCAGCACCCACATCTGGTGGCTCACCACCATCTATAACTTCAGCTCCAGGGGATCTGAGCCCTTTCTGGTCTCCACAAGCACTTACACACATGCACGTGGACACACACACACACACACACATGCATTCGCATATGTATATACACACATTTAAAAATAAGAACAAAATCTTTAAAAAAAGAAAAGAAAATCTGAGAGTGACCAACTAGAGCGTTTCTCCTCCTGCAG
Seq C2 exon
CCTGGATCTGAATGGCAGGAGGCCTGTGAGAGCTGCCGCTGTCTCCACGGGAAGAGTGTTTGCACTCAACACTGCCCAGAACTCAGCTGTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:98
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=WD(100=84.3),PF0009313=VWC=PU(14.3=11.4),PF053758=Pacifastin_I=PU(0.1=0.0)
A:
NA
C2:
PF0009313=VWC=FE(55.4=100),PF053758=Pacifastin_I=FE(91.2=100)
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:
TGGGGAAATATTGCAGCTTGGG
R:
CTGAGCACAGCTGAGTTCTGG
Band lengths:
295-810
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]