DreINT0132871 @ danRer10
Intron Retention
Gene
ENSDARG00000000189 | sema6e
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6E [Source:ZFIN;Acc:ZDB-GENE-040724-119]
Coordinates
chr16:30281960-30282433:+
Coord C1 exon
chr16:30281960-30282177
Coord A exon
chr16:30282178-30282301
Coord C2 exon
chr16:30282302-30282433
Length
124 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
TTTTTTTGTCCTCTTCTCAGCAT
3' ss Score
8.55
Exon sequences
Seq C1 exon
GTGGTGTTTTCCCGAGTGGCTCGCGTGTGTAAGAATGATAACGGCGGTTCTCCACGGGTTCTAGAAAGATACTGGACGTCTTTCCTGAAGGCCCGGTTAAACTGCTCAGTTCCTGGTGACTCTTTTTTCTACTTTGATGTTCTTCAGTCATTAACAAACGTCATGCAGATCAACCACAGGCCTGCAGTGTTGGGCGTCTTTACCACTCAAGCCAACAG
Seq A exon
GTACTGAATCCCAACACCCTAAGTTTTTGTGTTTCCATGCACTCTTCAACAAATGCTAAGCCTATTATGATAAAGCTTAATGAATTGGTTTGTTTGAAAGAGAGTTTTTTTGTCCTCTTCTCAG
Seq C2 exon
CATCACTGGTTCTGCTGTATGTGCATTTTACATGGATGACATAGAGAAAGTGTTCAATGGGAAGTTTAAGGAGCAGCGAAACAGCGAGTCCGCCTGGACACCAGTTCCTGATGAAGCGGTGCCCAAACCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000189:ENSDART00000135723:10
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=0.333
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.1=100)
A:
NA
C2:
PF0140314=Sema=FE(10.5=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:
CGGTTCTCCACGGGTTCTAGA
R:
CGCTGCTCCTTAAACTTCCCA
Band lengths:
252-376
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]