BtaINT0141494 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113482173-113483434:+
Coord C1 exon
chr4:113482173-113482340
Coord A exon
chr4:113482341-113483303
Coord C2 exon
chr4:113483304-113483434
Length
963 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
CTGCCTGCCTCCCCCTGCAGAGG
3' ss Score
11.59
Exon sequences
Seq C1 exon
AGGAGTGTGTGTGGAGCAGCTGGAGCAGCTGGACGCGGTGCTCATGCGAGGTGCTGGTGCAGCAGCGCTACCGACACCAGCGGCCCGCGCCCGGGGGCGCCGGGGCGGGCCCCCCCTGCACTCGACTGGACGGCCACTTCCGGCCTTGCCTCACGGGAAACTGCTCCG
Seq A exon
GTGAGGCCCCGGGAGCGAGGAGCCGGGGAGACGAACCCTGGCAGGGGCCTCCCGGGGTCCCCAGGGGGCACCGCCAGCTCCTCTTAGAGTGATACTCAGGGTGCCCAGGTCCTCAGAGGGGTGGCCCGCGCCTGCACGGACTCTGCCCTTGGCTGGGACCCTGCTCCAGCTGCTCCCTGCCTCACCCTCGCCCCCACCCTGCCCCACAAGCCTTCACCGTGGTTTTCTCACTTTGCAGCCACAGGCCCAGCTGTGCCTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTTTCTGTAGTTGCAGCAAGTGGGGGCTACTCTCTAGTTGCAGTGCTTGGTCTTCTCACTGCGGTGTCTTCTCTTGTTGCAGAGCACATGCTCTAGGGCACGTGGGCTTCAGTAGTTGCAGCACATGAGCTCTGTAGTTGTAGCTCTTGGTCTCTAGCGCACAAGCTCAATAGTTGTAGTGTACGGGCTTAGTTGCTTCTTGCCACATGGGAGCTTCCCAGACCAGGGATCGAACCTGTGTCTCCTGCATTGGCGGGTGGATTCTCTACCACTGAGCCACCAGGGAAGCCCCCCAGCTGTGGCTTTGTGTCCACTGGTAGCTGCCCCAGGCATGGTGGGTCTTTGCCCACTTATTACTCCAGCTGCCCTCCATCTCCACCCCTCTGCCTCCCACCTGCCAATCCTGGGAGCTACCTGCCAGGGCTTGAACCCCCTGCAGCCCGCTGGCTCTCCTGGGTCCAAACAGTTGGAGGTGCCTACAGGGACTGAGTGGGCATGGATGGGGCAACACTGGTCTGCCCTTACCTACTGCAGGGGGGCAGTATCCTGCACTCTTACTGGGTGACTTCAAGGGGAGGTGATGGGACCACGCACTGTGCCCTCTGGGTTTGGGGGGCAGATGGTGTCTCTGGGCTACACCCTGCACCAGCCTGTCTGCCTGCCTGCCTCCCCCTGCAG
Seq C2 exon
AGGACAGCTGTGCGCCTCCCTTCGAGTTCCAGGCCTGTGGCTCCCCCTGCACTGGACTCTGTGCCACATACCTGAGCCCTTGGCTCTGCCAGGACCTGCCGCCCTGCCAGCCTGGCTGCTACTGCCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:96
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0182612=TIL=PU(71.4=90.9)
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:
GAGTGTGTGTGGAGCAGCTG
R:
AAGGGCTCAGGTATGTGGCA
Band lengths:
247-1210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]