GgaINT0029097 @ galGal4
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:9408678-9409176:+
Coord C1 exon
chr10:9408678-9408809
Coord A exon
chr10:9408810-9409020
Coord C2 exon
chr10:9409021-9409176
Length
211 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CAATGTTGTTCTCCTTTCAGACC
3' ss Score
9.58
Exon sequences
Seq C1 exon
CATCCCTGGTTCAGCAGTGTGTGCTTTCAGCATGGATGACATTGAGAAGGTCTTCAAAGGGAGATTCAAAGAACAAAAAACTCCTGACTCTGTTTGGACAGCTGTACCTGAAGACAAGGTACCAAAGCCAAG
Seq A exon
GTAAAAAGTTTTTCCTTGTGGTACTATAAAGCTGTCCTTGTAAAGAGCTACTTTAAATCAGCTGCACTCTTGAGTGTTGTACTGGGTGGAAAAAAAAAAAAAAAAAGAGTAGAGCTTTACTCTTCAACCATAAGGATGCTCATTAGCAGGCTGCCTTCTCTCATTAACTGAAATACCAAGAGGGGAAAAAACAATGTTGTTCTCCTTTCAG
Seq C2 exon
ACCTGGCTGCTGTGCAAAACATGGCCTAGCAGAAGCTTACAAAACCTCCATTGATTTCCCAGACGAAACATTGTCCTTCATCAAATCTCATCCTTTGATGGATTCAGCTGTTCCCTCAATCATTGAGGAGCCTTGGTTTACCAAAACACGCGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.3=100)
A:
NA
C2:
PF0140314=Sema=FE(12.2=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:
CATCCCTGGTTCAGCAGTGTG
R:
GACGCGTGTTTTGGTAAACCA
Band lengths:
286-497
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]