BtaINT0141473 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113472995-113473737:+
Coord C1 exon
chr4:113472995-113473164
Coord A exon
chr4:113473165-113473690
Coord C2 exon
chr4:113473691-113473737
Length
526 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
TGTCTGCGTGCCCCGCCCAGCAC
3' ss Score
5.02
Exon sequences
Seq C1 exon
CACTGCGTTTGGCACTGCCAGCCCGGCTGTTACTGCCCCCCAGGCCAGGTGCTGAGTGCCGACGGCACCGTCTGCGTGCAGCCCGGTCACTGCAGCTGCCTGGACCTGCTGACTGGGGAGCGGCACCGTCCAGGGGCCCAGCTGGCCAAGCCTGACGGCTGCAACTACTG
Seq A exon
GTGAGGGCCGGTGGGGGCGAGGGGCGGCGTGCGGGCAGGATGCCACGGGTGAGGGCAGGGCTAGTCCACTCCGTATCTCACACACCTGAGCTCTCCCGGTCTCAGCTGATGCACACTAGGCTCCCACAAGCTCTGAGAAGATGCAGCAGGTACCCTAATCCCTGGTCTGACAGGTGGGGAATCTGAGGCAGCCAGCTCTGGGGATCTGGGAGACTTTGAAGAGCTGGGCTTGTGCTTTGAGGGGACAGGGGGTGGCGCTGTGGTGTTTCCTCCTGCTGTCTGGCTTCCTTTAGCCGCAGACGACCTGTGGTCACTTCCCCATAGGACTGAGTCCGCAGGATCCCTGGGCATGCCTGGAGTGGGTCAGGGAGCAGGGACTAGAGGTGCTGGAGAGTGGGGAGGGGGACTGAGACCTCAGAGGCTGGAGGTGGGGGAAAGGGGAAGGGGAGGCAGACAGGGAGGGGTGTGTTTGGAGGGCACGGTGCGAATGAGCTGCCCTCTCTCTCTGTCTGCGTGCCCCGCCCAG
Seq C2 exon
CACCTGCTCCGAGGGCCAGCTCACTTGCACAGACCTGCCTTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:77
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:
PF0182612=TIL=PD(54.5=52.6),PF053758=Pacifastin_I=PU(40.6=22.8)
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
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCCGGCTGTTACTGCC
R:
CTGGGCAAGGCAGGTCTGT
Band lengths:
198-724
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]