BtaINT0141496 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113483676-113484099:+
Coord C1 exon
chr4:113483676-113483800
Coord A exon
chr4:113483801-113484052
Coord C2 exon
chr4:113484053-113484099
Length
252 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CTGACCACCCCCTCCCACAGTGA
3' ss Score
7.48
Exon sequences
Seq C1 exon
GGGCTACTGGAGCAGGCCGGAGGCTGTGTACCCCCAGAACAGTGTAACTGCCAGCACGTCTCAGGAGAAGGAGCTGGGGTGACCCTGGCCCCTGGGGACCGCCTGCAGCTGGGCTGCAAAGAGTG
Seq A exon
GTGAGTGTTGGGGGTGAGGGAGGTGGCACCAGAGGCCTGGGACCAGGGACTGGACCAGGGAGGAGGAGGGGTTCCACAGGGTGGCCTGACCCCCGCAGAGAAGGCCAAGCAGAACCCCAAGGTCCCAGCCTCCCCCTGCTCCAAATGAGCCCAGAGTCCAGGTTACCCCTACATGAGCCCCCCACCCACCAACCCACCATTCTGGGCTGGGTCCTGCCTCCTGGAGCCCACCCTGACCACCCCCTCCCACAG
Seq C2 exon
TGAATGCCAGCGCGGGGAGCTACAGTGCACCAGCCAAGGCTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:98
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0182612=TIL=PD(25.0=33.3),PF053758=Pacifastin_I=PU(37.5=28.6)
A:
NA
C2:
PF053758=Pacifastin_I=FE(50.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTACTGGAGCAGGCCGGAG
R:
CTTGACAGCCTTGGCTGGTG
Band lengths:
169-421
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]