DreINT0132866 @ danRer10
Intron Retention
Gene
ENSDARG00000002748 | sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:ZFIN;Acc:ZDB-GENE-040426-1933]
Coordinates
chr19:409298-409660:+
Coord C1 exon
chr19:409298-409399
Coord A exon
chr19:409400-409569
Coord C2 exon
chr19:409570-409660
Length
170 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TGTTGTTTTGTTTTGTTCAGTTG
3' ss Score
8.64
Exon sequences
Seq C1 exon
GATGAATGTTACAATTATATCAAGGTTCTTGTTCCTCGTAATGACGAGACTCTGTTTGCCTGTGGAACAAACGCGCTGAATCCTGCCTGCCGCAACTACAGA
Seq A exon
GTGAGTAAACCACGCCAGCGCCCTCATGTGGAGAGAGAGAGAGTGTGTTTATTTGAGTTTAAGTGTGTGTGTTTGTGTATGAGAGTGTGAGTATGTGCTGTGTATGCGTGTGTGAGTATTTGTTTGTGTGTGTGTGTTGATATGCTGTTGTGTTGTTTTGTTTTGTTCAG
Seq C2 exon
TTGAGTTCACTGGAGCAGGTCGGACAGGAGCTCTTGGGTCAGGCAAGATGTCCATTTGAGTCTCGACAGTCCAATGTAGGAGTGTTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:6
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.5=100)
A:
NA
C2:
PF0140314=Sema=FE(7.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATATCAAGGTTCTTGTTCCTCGT
R:
CTGCAAACACTCCTACATTGGACT
Band lengths:
178-348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]