BtaINT0141449 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113461668-113462273:+
Coord C1 exon
chr4:113461668-113461832
Coord A exon
chr4:113461833-113462129
Coord C2 exon
chr4:113462130-113462273
Length
297 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
GGCTGCGGTGGCGCCCACAGGAC
3' ss Score
7.17
Exon sequences
Seq C1 exon
GCAAGGGGCCAGCGAGTCTTGGGTCCGAGCCTCACCCAAGTCCTGGGGGATCTGTGCAGACTGTGACCCCCACCTCCCAACCGGAGGCACAGGCCCTGAGACCGGAAATGGCAGCTGTGACGGTGCTCCCCCCACACCCCATGGTGACGCCCGAGGTTCCTGCTG
Seq A exon
GTGAGATGCCTCCTGCCCTGTAGAGACGGCGTCCCCGTAGAGGAACCGAGCCCCTGAGAGCTTGGCTGCTTTGCTCCAGGTCACATAGCTTGAGCTTAGGGGCTTGGGAGGATCAAGCCTAGGATCCAAGTCTCCCGAGACCACTCCCTGCTTTTCCGTAATCCCACGAGGGGCAGGCAGGGAGGGCACAGCGGATGTCAGGAGGGAGGCTGGGGGCTGCTAGGAGGTGACAGAGGAGAGAGGACAGGGCTGGGGAGGGGGCGATGGCCGGTCAGCTGGCTGCGGTGGCGCCCACAG
Seq C2 exon
GACGGAGCACCACGCCGGGGCCCTTCCCGCATGTGCAGTGCAGCCCAGGCCAGGTGCCCTGCGAGGTCCTGGGCTGCGTGGAGCTGGAGCAGCTGTGTGACGGGAGAGAGGACTGTCTGGACGGCTCTGATGAGAGGCCCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:54
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.265
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=75.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
CAGCGAGTCTTGGGTCCGAG
R:
CTCTCATCAGAGCCGTCCAGA
Band lengths:
292-589
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]