GgaINT1026466 @ galGal4
Intron Retention
Gene
ENSGALG00000004919 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr2:422849-423423:+
Coord C1 exon
chr2:422849-423074
Coord A exon
chr2:423075-423294
Coord C2 exon
chr2:423295-423423
Length
220 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
CAGCCCTCGCTCCCCACCAGAGC
3' ss Score
4.76
Exon sequences
Seq C1 exon
GTGCCAGAAGGGACGAGCGCGTGGCTCACTGTTGGCTCCACCAGCCCTGCTGTGCCATCCACCACCAGGCTGCCAGGTGTCCCCACCGCCACCATCACCCCCAGGGGGCCACCCTCTGCTGGTCCCCCATCACCTGGCATGGCAGCGGTAACGGTGTCACACCCTGTGACGGGACCACCTGCACTGCCCATGCCCCCCACTGGGGTCCCCACTCCAACATCTGCTG
Seq A exon
GTAAGGAGGCATGACCTGGCACCAGCCCTGCATGAGGTCCGAGGGGGGCACGACCTCCCCAGCATCTGGCACCACAGGAGTGGGGATATGAATGTCCCGAGGGTGATGTGGGGACAGCGCACAGCTTGCTGCTGGCTGGCTGCACTGTGGGGTGGGTGGTGATGGCCCAGGGGTCCCGCTTGTCCCACCAGCCCCCACCACAGCCCTCGCTCCCCACCAG
Seq C2 exon
AGCCACCCCTGCCCCGGCTCCTGTGCCCCCCGGACCAGTTCCTCTGTGATGCCCTGGGCTGTGTGGATGCAGCCATGGTCTGTGATGGGCAGCAGGACTGCCTGGATGGCTCTGATGAGGCGCACTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004919:ENSGALT00000007871:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.114
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCTCACTGTTGGCTCC
R:
CATCACAGACCATGGCTGCAT
Band lengths:
293-513
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]