RnoINT0133092 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116949847-116950155:+
Coord C1 exon
chr3:116949847-116949987
Coord A exon
chr3:116949988-116950077
Coord C2 exon
chr3:116950078-116950155
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
TTTGTTTGCTTTTTCGGCAGGTC
3' ss Score
9.32
Exon sequences
Seq C1 exon
GTGCAGCGCCGAGAGTGAGGAGGACAGGAAGGTCGTCTCGTTACAGCTGGACAGGGATCACCATGCTTTATACGTGGCCTTCTCCAGCTGCGTGGTCCGCATCCCCCTCAGCCGCTGTGAGCGCTATGGCTCCTGTAAAAA
Seq A exon
GTAAGCTTCCTTATTCGCTCCTGCTCCCAGGGTGGCTATCCTATGCTGAGGAGGAAAATCTGCATCACGCTTTGTTTGCTTTTTCGGCAG
Seq C2 exon
GTCTTGCATTGCATCACGAGACCCGTACTGTGGTTGGTTAAGCCAGGGAGTGTGTGAGAGAGTGACCTTAGGGATGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:13
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(1.5=12.5),PF0143720=PSI=PU(11.8=18.8)
A:
NA
C2:
PF0143720=PSI=FE(34.2=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:
TCGTTACAGCTGGACAGGGAT
R:
ACTCTCTCACACACTCCCTGG
Band lengths:
167-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]