BtaINT0141418 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113447216-113447620:+
Coord C1 exon
chr4:113447216-113447405
Coord A exon
chr4:113447406-113447525
Coord C2 exon
chr4:113447526-113447620
Length
120 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TTGTCCCTGGCCTCTGCTAGGAG
3' ss Score
5.82
Exon sequences
Seq C1 exon
TGTCTGCCAGGAGAGGGGCCTCTGGAACTGCACTGCTCACCACTGTGCTCCGCCCCGGACCTTCTGCCCCCGTGAGCTTGTCTATGTCCCTGGAGCCTGCCTCCTCACCTGTGACAGCCTTGATGCCGACCGCACCTGCCCCCCAGGCAGCCCGGGGGGCTGTGTCTGCCCCCCAGGCACCGTGCTGCTG
Seq A exon
GTATGTCTGGGAGGGGCTCCGCTAGCCAGTGCCCTGCCCTGGTCCCTGGCTGGGTGTAACTGGCAGGGAGGGGGCACCAGGCAGTCCTCCATGGAGCCCTTTGTCCCTGGCCTCTGCTAG
Seq C2 exon
GAGGAACGCTGCGTGCCTCCTGAGCTCTGTCCCTGCCGTCATGGCGGCCAGTGGTACCTGCCCAATGCTACAATCCAGGAGGACTGCAACCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:25
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(61.8=32.8),PF0182612=TIL=PU(78.8=64.1)
A:
NA
C2:
PF0182612=TIL=PD(17.3=28.1),PF053758=Pacifastin_I=PU(33.3=37.5)
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:
CTCTGGAACTGCACTGCTCAC
R:
TCCTGGATTGTAGCATTGGGC
Band lengths:
251-371
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]