GgaINT0095237 @ galGal4
Intron Retention
Gene
ENSGALG00000004919 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr2:441130-441515:+
Coord C1 exon
chr2:441130-441338
Coord A exon
chr2:441339-441419
Coord C2 exon
chr2:441420-441515
Length
81 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACTGAGCTCTCACCCCCCAGCCT
3' ss Score
5.29
Exon sequences
Seq C1 exon
CCTGTCCGGAGGGGGAGCGCTGGCAGGGCCCTGAGGTGCCACCAGGCTGTGAGCAGAGCTGCAGGGACATCCTCGATGAGACCCCTGCAAACTGCACCCCTTCCCCCTCCCCCGGCTGCACCTGTGAGCCCGGCCACTACCGCAACAGCAGCGGCCACTGTGTGCCCTCCACCCTCTGTGAGTGCCTGCACCAGGGGCAGCTCCACCAG
Seq A exon
GTGAGCAGAGCGCTGCACCGGGGGGTGCCCAGGGGTGCCTGGAGGTGCCCCCACCTCACTGACTGAGCTCTCACCCCCCAG
Seq C2 exon
CCTGGCAGCGAGTGGCAGGAGCAGTGCGCGAGGTGCCGCTGTGTGGATGGCAAAGCCAACTGCACCGATGGCTGCACGCCGCTCTCCTGTCCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004919:ENSGALT00000007871:99
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:
PF0182612=TIL=PD(88.1=84.3),PF0009313=VWC=PU(14.3=11.4),PF053758=Pacifastin_I=PU(2.7=1.4)
A:
NA
C2:
PF0009313=VWC=FE(55.4=100),PF053758=Pacifastin_I=FE(83.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATCCTCGATGAGACCCCTG
R:
GCACTGCTCCTGCCACTC
Band lengths:
170-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]