GgaINT1024752 @ galGal4
Intron Retention
Gene
ENSGALG00000001171 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:HGNC:10739]
Coordinates
chr28:2502230-2502634:-
Coord C1 exon
chr28:2502511-2502634
Coord A exon
chr28:2502360-2502510
Coord C2 exon
chr28:2502230-2502359
Length
151 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
CCCCCTCCTGTTGTCCCCAGATG
3' ss Score
12.92
Exon sequences
Seq C1 exon
CTGCCTGCACCAGGGGAGACAATGTGGCCCCCCCTCGTCCTGCTGCTCCTGCTCGCAGCGGAGAGGACGGCTCACGGCACCTTCCCCGAGGAGCCCAACCCCATCGCCGTGGCAAACGAGGACT
Seq A exon
GTGAGTGCCTGGGGAGGGGGCCAGGGGGGCACAGATGGGTGCAGAGAGGGGACGGGGCTGGGGGGCTCGGGGTGCTCTGTGAGTAGGGTGCTGGCTGGCCGTGGGGCTGTGTGTGATGCTATCTCCATGCCCCCCCTCCTGTTGTCCCCAG
Seq C2 exon
ATGTGAAGCACTACGCCGTGTTCGTGGGCCATGGCAGCAGCCGGCCGGGCGGCCCCGAGGGCGGTGGCACCGAGCGCCTCAACATCCAGCGCATCCTCAAGGTCAACCGGACCCTCTTTGTTGGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001171:ENSGALT00000001774:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.179 A=NA C2=0.330
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(25.8=36.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCAGGGGAGACAATGTG
R:
GTCTCCAACAAAGAGGGTCCG
Band lengths:
246-397
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]