RnoINT0143940 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78099372-78100187:+
Coord C1 exon
chr4:78099372-78099499
Coord A exon
chr4:78099500-78100027
Coord C2 exon
chr4:78100028-78100187
Length
528 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
GCGAGTAATATCTTCCACAGCCT
3' ss Score
2.78
Exon sequences
Seq C1 exon
GCATCATGGTGCAGAGGGCTGGCTCCTCTGCTGCGTATATCTCCAACTTGTCGCTCCAGTTCAGCAGTGACGGTCTACAGTGGCACAGCGTTCTCAACTCTCTGTCTAGTACCCTGCCTCCACCCAAG
Seq A exon
GTACTGAGCCCTCTGCTGCCCTGGGGCAGGTGGCCAAACGAACTCCTTTGTGGATACCACAGCCTTTGTCCCCAAGGCACTTCCATTCCCCTGGCAGGCAGTCCTTGCTTTAGACATCTGTGGGACACCTTCTAACTAGCAGAGACAATGTTCTGTAGAGTTGAGAGTCCAGGGACATCTGAAAACCCCAGAGTGGCTTACAGTCTGCATACATGCCCCTCTATACCAGGCTGTGAAGGAGCAGGGTGGGAACACAGCCAGTCACAGAGGCCCTTGAAGCACAGGCCTCTGGAGCAGCCTTGGCGTGCACTATTTCTTTAGGAGTGGGCACTCTCCTCAGGACGACAGGCCCCTGCAGCCATAGGAATCAGCTCACTCATGTCCGCTCTCCTTAAAGAGCATCTGCTCTATGTGGGAATGACACCCATGTCATGAGGGTTGGGGGACTCAGAAGGGACATCAGGGCAGAGTTACAATGGCAGCTTGAGCAAGAGGTAGGACTTGGGCAGCGAGTAATATCTTCCACAG
Seq C2 exon
CCTTCTCCGGAGAGCTCGAACCACATGGTCCCTGAGGTATGGACATTCGACCAGATGGTACAGGCAAGGTACATCAGGGTGTGGCCACATGGCAGCCACCTCAGAGACAACAACCAGCAGGATATCTTCCTGTGGGTGGAGCTACTGGGCTGTAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.163 A=NA C2=0.204
Domain overlap (PFAM):
C1:
PF0075420=F5_F8_type_C=FE(33.9=100)
A:
NA
C2:
PF0075420=F5_F8_type_C=PD(37.9=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCATGGTGCAGAGGGCTG
R:
TTACAGCCCAGTAGCTCCACC
Band lengths:
282-810
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]