BtaINT0141439 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113455849-113456209:+
Coord C1 exon
chr4:113455849-113456002
Coord A exon
chr4:113456003-113456154
Coord C2 exon
chr4:113456155-113456209
Length
152 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCCGGCTCTTGCATCCGTAGGAC
3' ss Score
10.35
Exon sequences
Seq C1 exon
GTGCCAGACAGAGCCCTGTGAAGGCTGCGAGCAGGACGGCCGGGTCCACCGCGTGGGGGAGCGCTGGCGAGCGGGCCCCTGCAGGGTCTGCCAGTGTCTGCACGACGGCTCGGCACGCTGCTCCCCCTACTGCCCACTGGGCAGCTGCCCCCAG
Seq A exon
GTGAGGCGGGCCAGGGGGCGCCCAGGTGGCCAGCAGGGGTGGGGCGAGGAGCGGTGTGTAGAGGCCAAAATTGTGGGTGGCAGTTGATGGAGCGGGCCGGGGACGGGCAGGTGGCCAATTCCGCACGTCCAGCCCGGCTCTTGCATCCGTAG
Seq C2 exon
GACTGGGTTCTGGTGGAGGGAGTGGGGGAGTCGTGTTGCCACTGCGTGCCGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:45
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:
PF0009313=VWC=PU(72.4=80.8)
A:
NA
C2:
PF0009313=VWC=PD(24.1=73.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCCAGACAGAGCCCTG
R:
GGCAACACGACTCCCCCA
Band lengths:
194-346
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]