BtaINT0141451 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113462945-113463388:+
Coord C1 exon
chr4:113462945-113463124
Coord A exon
chr4:113463125-113463223
Coord C2 exon
chr4:113463224-113463388
Length
99 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGG
5' ss Score
4.2
3' ss Seq
CGGCCGGCCCGTCCCTGCAGTGG
3' ss Score
8.1
Exon sequences
Seq C1 exon
CATGGGCAGCGGGCACCGTGCCCTTCACCGTGCCCACCACCACCCTGCCGGGGTTGCCGGCCTCCAGGGACCTCTGCTCCCCGAGCCAGCTGACCTGCGGCAGTGGGGAGTGTCTGCCTGCCGAGCGGCGCTGCGACCTGCAGCTGGACTGCCAGGACGGCTCGGACGAGAATGGCTGTG
Seq A exon
GTAGGGGCGAGGCTGGTCCGGGTCAGGCCGGGGGCCGCCCTGGGGAGGGCCCGCTCCCGCGTGAGTCCCTCTCTGAACTCGGCCGGCCCGTCCCTGCAG
Seq C2 exon
TGGACTGTGGCCTGGCGCCCTGGTCTGGCTGGAGCAGCTGCAGCCGTAGCTGTGGCCTGGGCCTCGCCTTCCAGCGCCGGGAGCTACTGCGGCCGCCCCTGCCCGGGGGCAGCTGCCCACCGGACCGGCTCCGCAGCCAGCCCTGCTTCGTGCAGGCCTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:56
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.066 A=NA C2=0.054
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=PU(92.5=60.7)
A:
NA
C2:
PF0005713=Ldl_recept_a=PD(5.0=3.6),PF0009014=TSP_1=WD(100=87.5)
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:
CTCGGACGAGAATGGCTGTG
R:
ACGAAGCAGGGCTGGCTG
Band lengths:
171-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]