RnoINT0133058 @ rn6
Intron Retention
Gene
ENSRNOG00000045998 | Sema6b
Description
semaphorin 6B [Source:RGD Symbol;Acc:69278]
Coordinates
chr9:10946915-10947591:+
Coord C1 exon
chr9:10946915-10947046
Coord A exon
chr9:10947047-10947441
Coord C2 exon
chr9:10947442-10947591
Length
395 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACA
5' ss Score
5.49
3' ss Seq
GACTCACTGTCTTCACCCAGGCC
3' ss Score
7.5
Exon sequences
Seq C1 exon
CATCCCTGGCTCAGCTGTCTGTGCCTTTGACATGAACCAAGTGGCTGCTGTGTTTGAAGGCCGCTTCCGGGAGCAGAAGTCACCTGAGTCAATCTGGACCCCAGTGCCTGAGGACCAAGTACCACGGCCCAG
Seq A exon
GTGACAGTGACTTCCATCTTCACAGGGTAGTCAAGGAGTGTTCTGCCCCTACAATGGCTGGTCACTGTGTCAGATAAGGAGAGCAATGGAGGGAAACAAAGAAGCTTGTGGAGGAAGCGACACTAGGAGGCTGGCACAAAGGGCCAGGCACTCAAGGATCTTCATTTGTTGAGGGATAAGCTGGGCAGAGGGTGAAAATGTGCACAAAGGCCCTGGACTAGGGGGCGTGGCCTGTGTGAGGCCCAGGCAAATCAGATCAGAATGTAAAGAGGTGCTGAGGCTACAGAGAATCAGATCAGGGAAACCATAAAAGTGGGGAGCCCCAAGATGCCCCAGGGAATCAGGGCGTCATTGTGGTATCCTGGCATCCTCCCTGACTCACTGTCTTCACCCAG
Seq C2 exon
GCCCGGGTGCTGTGCAGCGCCCGGTATGCAGTACAACGCATCCAATGCCCTTCCTGACGAGATTCTCAACTTTGTAAAGACCCACCCACTGATGGACGAAGCGGTGCCCTCCCTGGGCCACTCGCCTTGGATTGTGAGAACTCTGATACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000045998:ENSRNOT00000070794:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.267 A=NA C2=0.039
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.4=100)
A:
NA
C2:
PF0140314=Sema=FE(11.8=100)
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:
CATCCCTGGCTCAGCTGTCT
R:
TCAGAGTTCTCACAATCCAAGGC
Band lengths:
278-673
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]