BtaINT0141392 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113484406-113485147:+
Coord C1 exon
chr4:113484406-113484684
Coord A exon
chr4:113484685-113484988
Coord C2 exon
chr4:113484989-113485147
Length
304 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATG
5' ss Score
5.22
3' ss Seq
CTCCCGTTTTCTCTCCCCAGACT
3' ss Score
11.7
Exon sequences
Seq C1 exon
GTCTTCTGCCTCTGAGCGGCTGGTCTGAGTGGTCACCCTGTGGGCCCTGCCTGCCCCTCGGCCTGCTGGCCCCTGCCTCCAGGGCTGCCCTAGAGGAGCGCTGGCCCCAGGACACAGCTGGCCTGTCCCCCACCTCGGCCCCCACGCTGGCTTCGGAGCAGCACCGCCACCGCCTCTGTTTGGACCCTGAGACAGGGAGGCCGTGGGCCGGGGACCCAGACCTCTGCACTGTGCCCCTCAGCCAACAACGCCTCTGTCCAGACCCTGGAGCCTGCCAAG
Seq A exon
GTGATGGGGGAGGCGGGCCACGTGGGGACGGGGCCCGTGGGGGCGGGGCCATGTGGGGCTGGGGATGGGCGGGGTCTGGTAAGGGGCGGGGCCTGGCCGGGTAGGGCTGGGCTCCGCTATTCATGTCTGTTGGTGGGGGGGCCCTTAGCTGGCTGGCTCATCCTCCTGCTAGACTCCAGGGTCTGCTGGATTTGAGGTTGGGAGGGGGCAGCAGCTGGAAGAGGAGGAAGGGGACTCAGGGCTGCAGAGGGAGCCAGGGGGCGGGGGGTGGGCCTGGACACTGACTCCCGTTTTCTCTCCCCAG
Seq C2 exon
ACTTATGTCAGTGGGGTCCCTGGGGGGCCTGGAGCCCCTGCCAGGTGCCCTGCAGTGGGGGATTCCGGCTGCGCTGGAGAGAGGCCGGGATCCCCCCTGGAGGAGGCTGCCGGGGGCCATGGGCTCAGACTGAGAGCTGTAACATGGGGCCTTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:100
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.234 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF053758=Pacifastin_I=PD(9.4=3.2)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.0),PF0182612=TIL=PU(14.3=18.5)
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:
CTGGTCTGAGTGGTCACCCTG
R:
GATCCCGGCCTCTCTCCAG
Band lengths:
352-656
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]