BtaINT0141400 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113487247-113487867:+
Coord C1 exon
chr4:113487247-113487462
Coord A exon
chr4:113487463-113487771
Coord C2 exon
chr4:113487772-113487867
Length
309 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
GTTCTGCCCCCCTTCCCCAGCCG
3' ss Score
8.4
Exon sequences
Seq C1 exon
TGCCCCCCCGGAGAAACGTGGCAACACGTGGCCCCCGGGGAGCTGGGGCCCTGCGAGCAGACGTGCCGGGAACCCAACGCCACAGAGACCCAGGGCAACTGCAGTGGGAGGCAGGCCCCGGGCTGTGTGTGCCAGCGCGGGCACTTCCGCAGCCAGGAGGGCCCCTGCGTGCCCGTGGATCTCTGCGAGTGCTGGCACCATGGGCGCCCCCACCTG
Seq A exon
GTGAGCCACTGTGGCCCTCAGTGCCCCCTGGCCCTTCCTGACCCAGGGCTCTGGACTACTGGTTTGTCCCTGGCTCCTACCCCTGTACCCGGACCCGCAGCAGCAGGCAGCTTGGCCAGCGGCTGGCACACTTGGACCATCTCTGGCCCCCAGGGGCCCACCTCCCTCCTGAAACCCTTGCTGCCGACGCTGGTCTCAGGCCACTGCCCTGGCCAGGCCCCTGGGTGGGCTCGGGGTGGGGGCTGGGTAACAGAAAAGTCTGTGATGGGGAGGGGGGTGTGGAGAGCAAGTTCTGCCCCCCTTCCCCAG
Seq C2 exon
CCGGGATCCGAGTGGCAGGAGGCCTGTGAGAGCTGCCGCTGCGTCAGCGGGGAGAGTATCTGCACCCAGCACTGCCCCCCGCTCACCTGTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:108
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0182612=TIL=WD(100=86.1),PF0009313=VWC=PU(14.3=11.1),PF053758=Pacifastin_I=PU(0.1=0.0)
A:
NA
C2:
PF0009313=VWC=FE(55.4=100),PF053758=Pacifastin_I=FE(86.1=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:
CCCGGAGAAACGTGGCAAC
R:
CTGGGTGCAGATACTCTCCCC
Band lengths:
279-588
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]