GgaINT0029096 @ galGal4
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:9408352-9408809:+
Coord C1 exon
chr10:9408352-9408569
Coord A exon
chr10:9408570-9408677
Coord C2 exon
chr10:9408678-9408809
Length
108 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CTCTTTTTCTTATTTTACAGCAT
3' ss Score
11.23
Exon sequences
Seq C1 exon
GCTGTGTATTCCCGTGTGGCACGCATATGCAAAAATGACATGGGGGGTTCCCAGAGAGTACTGGAAAAACATTGGACATCCTTTCTGAAAGCTCGGCTCAACTGCTCCGTTCCTGGGGATTCGTTCTTCTACTTTGATGTTCTACAGTCTATCACGGACATAATAGAAATCAATGGAATCCCCACGGTTGTCGGTGTATTCACTACACAGCTTAACAG
Seq A exon
GTGAGAGATGAGCAACTTTACATCAAAGGTAGTTCTCTGGTTCTCTCTTGCACTGAGATTGGTGCTATTGTAGGCTGAGTTCTTGCAACTCTTTTTCTTATTTTACAG
Seq C2 exon
CATCCCTGGTTCAGCAGTGTGTGCTTTCAGCATGGATGACATTGAGAAGGTCTTCAAAGGGAGATTCAAAGAACAAAAAACTCCTGACTCTGTTTGGACAGCTGTACCTGAAGACAAGGTACCAAAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:9
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=0.111
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(16.9=100)
A:
NA
C2:
PF0140314=Sema=FE(10.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTTCTGAAAGCTCGGCTCA
R:
TGTCTTCAGGTACAGCTGTCCA
Band lengths:
255-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]