RnoINT0133102 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116947649-116948116:+
Coord C1 exon
chr3:116947649-116947866
Coord A exon
chr3:116947867-116947984
Coord C2 exon
chr3:116947985-116948116
Length
118 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
GTTTTCTTCCCCCTTTACAGCAT
3' ss Score
10.78
Exon sequences
Seq C1 exon
GCTGTGTACTCCCGAGTGGCCCGCATTTGTAAAAACGACATGGGTGGCTCACAGCGGGTCCTGGAGAAACACTGGACTTCCTTCCTGAAGGCTCGGCTTAACTGCTCAGTCCCTGGAGATTCCTTTTTCTACTTCGATGTTCTGCAGTCCATCACAGACATCATCCAAATCAATGGCATCCCCACCGTGATCGGGGTCTTCACCACGCAGCTCAACAG
Seq A exon
GTGGGGACAAGCAGAACCCGAGTCCCCGCCACCCCACGGAGGCTCTGTGCTCCCCGTGGGAACTGGGCATGGCCCCCACTGTCATCCTCGTCCTCATGGTTTTCTTCCCCCTTTACAG
Seq C2 exon
CATTCCTGGCTCTGCAGTCTGTGCCTTTAGCATGGACGACATTGAGAAAGTGTTCAAAGGGCGGTTCAAAGAGCAGAAAACCCCAGACTCTGTTTGGACAGCGGTTCCTGAAGACAAAGTACCAAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:9
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=0.111
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.8=100)
A:
NA
C2:
PF0140314=Sema=FE(10.9=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:
CCTGAAGGCTCGGCTTAACTG
R:
TTCAGGAACCGCTGTCCAAAC
Band lengths:
247-365
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]