RnoINT0133090 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116948434-116948848:+
Coord C1 exon
chr3:116948434-116948589
Coord A exon
chr3:116948590-116948674
Coord C2 exon
chr3:116948675-116948848
Length
85 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
TGCCTCTTTTCCTGCTCTAGGTA
3' ss Score
11.63
Exon sequences
Seq C1 exon
GCCTGGCTGTTGTGCCAAACATGGCCTCGCGGAAGCTTACAAAACCTCCATCGACTTTCCAGATGATACCCTGTCTTTCATCAAGTCCCACCCGCTGATGGACTCCGCTGTCCCACCCATTGCTGATGAGCCCTGGTTCACAAAGACTCGGGTCCG
Seq A exon
GTGAGACAATAGGCCAGTCTACTCCCACCCATTTCTCTTCCACAGGTCTCCGGATCGGACTGACCTGCCTCTTTTCCTGCTCTAG
Seq C2 exon
GTACAGGCTGACAGCCATCGAAGTGGACCGTTCGGCAGGGCCGTACCAAAACTACACAGTCATCTTTGTTGGCTCTGAGGCCGGCGTGGTGCTTAAAGTTTTGGCAAAGACCAGTCCTTTCTCTTTGAACGACAGTGTATTACTCGAAGAGATCGAAGCTTATAACCCAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:11
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(12.9=100)
A:
NA
C2:
PF0140314=Sema=FE(14.4=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:
GTCCCACCCATTGCTGATGAG
R:
AGAAAGGACTGGTCTTTGCCA
Band lengths:
169-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]