RnoINT0133060 @ rn6
Intron Retention
Gene
ENSRNOG00000045998 | Sema6b
Description
semaphorin 6B [Source:RGD Symbol;Acc:69278]
Coordinates
chr9:10947896-10948313:+
Coord C1 exon
chr9:10947896-10948078
Coord A exon
chr9:10948079-10948163
Coord C2 exon
chr9:10948164-10948313
Length
85 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGA
5' ss Score
5.06
3' ss Seq
GGTTCACCCCGTGTGCCCAGGTG
3' ss Score
5.78
Exon sequences
Seq C1 exon
GCACCAGCTGACCCGAGTGGCTGTGGATGTGGGTGCAGGCCCATGGGGCAATCAGACAATAGTCTTCCTTGGCTCTGAGGTTGGCACAGTCCTCAAATTCCTTGTGAAGCCCAATGCCAGTGTCTCAGGGACCACAGGGCCCAGCATCTTTTTGGAGGAGTTTGAGACCTACCGGCCAGACAG
Seq A exon
GTCTGAGGATAAGCAGGGAGGTGGGAGTGACTGGCTGAACCATGGGGTGGGCATACCAGCCTCATGGTTCACCCCGTGTGCCCAG
Seq C2 exon
GTGTGGACGATCCAGCAGTGCTGGTGAGTGGGGACAACGACTTCTGAGCCTGGAGCTAGATGCTGCCTCAGGTGGCCTGCTGGCAGCCTTCCCCCGCTGTGTGGTTCGTGTTCCTGTTGCCCGCTGCCAGCTGTACTCGGGGTGCATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000045998:ENSRNOT00000070794:12
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(14.5=100)
A:
NA
C2:
PF0140314=Sema=PD(0.2=2.0),PF0143720=PSI=PU(16.1=17.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCCTTGGCTCTGAGGTTGG
R:
TCAGAAGTCGTTGTCCCCACT
Band lengths:
167-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]