GgaINT1026455 @ galGal4
Intron Retention
Gene
ENSGALG00000004919 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr2:417380-417873:+
Coord C1 exon
chr2:417380-417610
Coord A exon
chr2:417611-417687
Coord C2 exon
chr2:417688-417873
Length
77 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CACTGTCCCCTTCCCCACAGACC
3' ss Score
11.95
Exon sequences
Seq C1 exon
GCTGCAGTCCAAGCTGCAGTGCGGGTGAGTTCCAGTGTGCGGCGGGACGCTGCGTGCCATACCCACACCGCTGCAATGGACACGACGACTGCGGGGACTTCAGCGATGAGCGGGGCTGCGTCTGCCCAGCCGGCCACTTCCAGTGCCCTGATGCACAGTGCCTGCCCCCGGCTGCCCTCTGTGATGGGATGCAGGACTGCGGGGATGGCACCGATGAGGCGTTCTGCCCAG
Seq A exon
GTGAGGGGCTGTGGCTGTGGTGAGCACGGGGCTGAGCGCCTGGTGACATAGCCCTGGCACTGTCCCCTTCCCCACAG
Seq C2 exon
ACCGCATCACCTGTGCCCCAGGACAGCTCCCCTGCCCCGATGGTTCATGTGTCAGCCAGGTGAAGCTCTGTGATGGCATCTGGGACTGCAGAGATGGATGGGATGAGAGATCTGTGCGCTGCATGGTGTCCTGGGCCCCCCCCGCACCCACCCAGCTGCCCACAGTGCCTGCTAACGGCACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004919:ENSGALT00000007871:30
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=0.063
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=PD(2.6=1.3),PF0005713=Ldl_recept_a=WD(100=47.4),PF0005713=Ldl_recept_a=WD(100=46.2)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=61.9)
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:
TCTGTGATGGGATGCAGGACT
R:
CAGCGCACAGATCTCTCATCC
Band lengths:
175-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]