GgaINT0029100 @ galGal4
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:9410009-9410334:+
Coord C1 exon
chr10:9410009-9410149
Coord A exon
chr10:9410150-9410256
Coord C2 exon
chr10:9410257-9410334
Length
107 bp
Sequences
Splice sites
5' ss Seq
AAAGTACGG
5' ss Score
4.86
3' ss Seq
TTGTTTTTTTCTCTTGCAAGGGC
3' ss Score
7.66
Exon sequences
Seq C1 exon
GTGTAATGCTGAGAGCGAGGAAGACAGAAGAGTCATTTCCCTTCAGCTGGATAGAGACCACCATGCTCTGTTTGTGGCGTTCTCCAGCTGTGTCGTTAGAATTCCTCTGAGCCGGTGTGAGCGTCACGGGTCATGTAAAAA
Seq A exon
GTACGGCTCCGTTCCTAAACTCCCCTTAAAGGAAGGGTGCCAACATCTCTAGGGAAGGAAGTAAAAAAAAATGCATGATTTTTTTGTTTGTTTTTTTCTCTTGCAAG
Seq C2 exon
GGCATGTATTGCTTCTCGGGATCCATACTGTGGCTGGTTAGACCACGAGGAGTGTGGGAGAGTGACGCCAGGCATGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:13
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=0.074
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(1.2=10.4),PF0143720=PSI=PU(15.0=18.8)
A:
NA
C2:
PF0143720=PSI=FE(43.3=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:
GCTGAGAGCGAGGAAGACAGA
R:
CATGCCTGGCGTCACTCTC
Band lengths:
210-317
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]