BtaINT0141463 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113468840-113469227:+
Coord C1 exon
chr4:113468840-113468886
Coord A exon
chr4:113468887-113469056
Coord C2 exon
chr4:113469057-113469227
Length
170 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
CCCCACACCCACCCTGGCAGTGG
3' ss Score
3.35
Exon sequences
Seq C1 exon
CACCTGTATCTCTGGTGAGATGGTGTGTGCCTCGGAGCCCTGCCCAG
Seq A exon
GTACCCCCATACTCGGGGCCAAGGAATTGGCAGTGGTTGGGTCTCAGGGATTCTGGTCCCTTCAGTAATCAACCTGGTGGTGTCGGGGGTGCCTTCAGGAAGTTGGGGTCCAGGGAGGACTTGACCTGTCTCACACATCCCGTGTCTCTCCCCCACACCCACCCTGGCAG
Seq C2 exon
TGGCCTGTGGCTGGAGCCCCTGGACCCCGTGGAGTCTCTGCAGCCGCAGCTGTAACGTGGGCGTTCGGCGGCGCTTCCGGGCGGGCACAGCTCCCCCTGCTGCCTTCGGGGGGGCTGCGTGCCAGGGCCCCAACATGGAGGCTGAATTCTGCAGCCTGCGGCCATGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:68
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:
NO
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
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:
CTCTGGTGAGATGGTGTGTGC
R:
CAGGCTGCAGAATTCAGCCTC
Band lengths:
196-366
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]