BtaINT0141465 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113439835-113440163:+
Coord C1 exon
chr4:113439835-113439993
Coord A exon
chr4:113439994-113440083
Coord C2 exon
chr4:113440084-113440163
Length
90 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TCTGCCTCAACCTCCCCCAGATG
3' ss Score
8.55
Exon sequences
Seq C1 exon
GGCTCAGCCTGCAGTGGCAAGGGGACTGGCTGGTGCTGTCGGGAGGCCTGGGGGTCGTTGTGCGGCTGGACCGGTCCAGTTCCGTCTCCATTTCTGTGGACCAGGAGCTCCAGGGACAGACTCAAGGCCTCTGTGGGGTCTACAACGGCCAGCCTGAGG
Seq A exon
GTGAGTGGGGGTGAGGCTTGGTTGCTGCTGTGGGAAGGAAGGGGAGACAGGAGTCCCCAGACACAGCCGCTCTGCCTCAACCTCCCCCAG
Seq C2 exon
ATGACTTCCTAGAGCCTGGCAGGGGACTGGCTGCGTTAGCTGCCACCTTTGGGAATTCCTGGAGACTCCCAGACTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF0009420=VWD=FE(36.1=100)
A:
NA
C2:
PF0009420=VWD=PD(4.8=25.9)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCAGTTCCGTCTCCATTT
R:
CTCTGAGTCTGGGAGTCTCCA
Band lengths:
167-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]