GgaINT0029088 @ galGal3
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
NA
Coordinates
chr10:11364387-11364988:+
Coord C1 exon
chr10:11364387-11364495
Coord A exon
chr10:11364496-11364876
Coord C2 exon
chr10:11364877-11364988
Length
381 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TAGCCCACTTTTACTTGCAGATT
3' ss Score
6.9
Exon sequences
Seq C1 exon
ATGAGGCTTCCTCTGCTGTGCGCCTCTGTGATGCTAATGAGTCTGTCCCAGTGCCGAGCTGTCAGCTTTCCTGAAGATGAGGACCCTATTAACATTGTTGACTACCACT
Seq A exon
GTAAGTAATCTGCAAATGGTGCCAGCCAGTAGGGAGAGGCTTGCAATGCTTGCTTCTTTCTTTATTTTTTTTTTTTTTAAGTCCCTGGGAAGTTAAGAAAAAGATCTGTTTCCTTTCAAATTGAAATGTGTTTACTGGCTTTGTATCTTTAATAGAACACTTAATCATTTTCTTAAAAAAGCAATCAGAAATACAGCAATAACTTCAGGAAAAAGAACATTTGCTGACATTAGCCATCTTTTTTTCATTTATATTCAAGACATTACTCAAGGAATTTAGTTTAAACCCTTCTACACCTAGTATATACAGCTAATCAATGCCATATATTGATTCTTTAGCTCTATAATCCTGAGTGATGGTGTAGCCCACTTTTACTTGCAG
Seq C2 exon
ATTCAAGGCAATATCCAGTATTTAGAGGACGCCCTTCAGGCAATGAATCTCAGCACAGACTGGACTTCCAACTGATGCTGAAAATTCGAGACACACTTTATATCGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.053
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(3.7=42.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCTTCCTCTGCTGTGC
R:
TGCCAGCGATATAAAGTGTGTCT
Band lengths:
218-599
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]