BtaINT0141429 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113451283-113451880:+
Coord C1 exon
chr4:113451283-113451516
Coord A exon
chr4:113451517-113451695
Coord C2 exon
chr4:113451696-113451880
Length
179 bp
Sequences
Splice sites
5' ss Seq
TGGGTTAGT
5' ss Score
3.1
3' ss Seq
GCCCCTCTCTCTGGCTACAGGGC
3' ss Score
9.86
Exon sequences
Seq C1 exon
GCTGTGCCACCCCGGTCTGTGGCGAGGGGCAGGTGTCTTGCAGCTCCGGCCGCTGCCTGCCCCTGGTCCTGCTCTGTGATGGGCAGGACGACTGTGGAGACGGGATGGATGAGCAGGGCTGCCCGTGCCCCCAGGACTCGCTGACCTGTGCCGACGGGCACTGCCTGCCCCCGGCCCGGCTCTGTGACGGGCACCCCGACTGTCCGGATGGTGCTGACGAGGAGTCTTGCCTGG
Seq A exon
GTTAGTGGTCCCTATCCCGGGCTCCAGCCCACGAGGCATCTGTCTCGTGAGCCCCAACCTGCCTGCCTCCCCTCCTTCACCAATGCAGGTTCCTGCTGAGAAGTGGGCACCTGTGGGCATGTTAGAGAGGGCATCCCAAGGAGCAGTACCCTGGGACCAGCCCCTCTCTCTGGCTACAG
Seq C2 exon
GGCAAGTGGACTGCGCCCCTGGGGAGGTGTCCTGCGTCGATGGTACCTGCCTGGGGGCCATCCAGCTGTGTGATGGAGTCTGGGACTGTCTGGATGGTGCCGATGAGGGGCCTGGGCACTGCCCCCTCCCCTCTCTGCCCACTCCTCCTGCTGGTACCTTGCCTGGCCCCTCTGCTGTCTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:35
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=0.306
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=PD(2.6=1.3),PF0005713=Ldl_recept_a=WD(100=46.8),PF0005713=Ldl_recept_a=WD(100=45.6)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=62.9)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGTGGAGACGGGATGGAT
R:
CCATCCAGACAGTCCCAGACT
Band lengths:
242-421
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]