BtaINT0141420 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113447876-113448610:+
Coord C1 exon
chr4:113447876-113448132
Coord A exon
chr4:113448133-113448475
Coord C2 exon
chr4:113448476-113448610
Length
343 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGCT
5' ss Score
1.4
3' ss Seq
ATGCCTCTGCTCCCCCACAGGCA
3' ss Score
10.8
Exon sequences
Seq C1 exon
CGTGTGCCAGGGTCAGCAGTGGCACTGCACGGGCCAGCGGTGCGATGGACGGTGCCGGGCGTCAGGCGCCCCTCACTATGTGACGTTCGACGGGCTGGCCCTCACCTTCCCCGGGGCCTGCGAGTACCTGCTGGTGCGAGAGGCCAGTGGCCAGTTCATGGTCTCCGCCCAAAACCTGCCGTGCGGAGCCAGTGGCCTCACCTGCACCAAGGCGCTGACTGTGCGGCTGCAGGGCACCGTTGTGCACATGCTCAGAG
Seq A exon
GTGGCTGTGACATTGAAGGATGACGTGGGCCAGGGAGGAGGGCCTCCACCCGGGTGGCATCACAGCTCTGCGGGAACAGCTGAGGCCTGGGGTTTCACACATCTCCCCACTGCTAGCCATCAGTCCCGGGGTGGGGAGCTGGTGACTCTTCTCTTGGTTGGGAATCCTGATTCTGGAAGGCTCCAGGAAATTAAAGCCCAGAGAGGTCTAACGATTTGCTCCAAGTCACATGGCTGGAGAAGCAAAGGAAAGGCTGGAGGGGAGGGAGGCTGGGAGGGCCTCATGGGGATCTCGGAGCCCCTGGACCCTGAGGCCGGGCCTGAATGCCTCTGCTCCCCCACAG
Seq C2 exon
GCAGGGCAGTGATGGTGAATGGGGTGAGTGTGACGCCCCCCAAGGTCTACTCAGGCCCCGGGCTGAGCCTGCACACCGCCGGCCTCTTCCTGCTTCTCAGCACCCACCTGGGCCTCACCTTGCTCTGGGATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:27
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:
PF053758=Pacifastin_I=PD(63.9=26.4),PF0009420=VWD=PU(45.3=78.2)
A:
NA
C2:
PF0009420=VWD=FE(30.0=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:
AGGGTCAGCAGTGGCACT
R:
GCTGAGAAGCAGGAAGAGGC
Band lengths:
350-693
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]