RnoINT0132812 @ rn6
Intron Retention
Gene
ENSRNOG00000016512 | Sema3b
Description
semaphorin 3B [Source:RGD Symbol;Acc:1310079]
Coordinates
chr8:116356905-116357200:-
Coord C1 exon
chr8:116357131-116357200
Coord A exon
chr8:116357050-116357130
Coord C2 exon
chr8:116356905-116357049
Length
81 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GCTGTCCTTGTTGCCTCCAGTGG
3' ss Score
7.69
Exon sequences
Seq C1 exon
AGGATGTTTTCCTTTTGTCCTCCCGAGACCGCCAGACACCTTTTCTCTATGCTGTCTTCTCCACCTCCAG
Seq A exon
GTGAGGGGCAGGTAGCAGTTCCCTTGGGCAGTCAGTTGAGCCTGCTGGGGTTGCTCACTTCGCTGTCCTTGTTGCCTCCAG
Seq C2 exon
TGGCATCTTCCAGGGCTCTGCTGTGTGCGTGTACAGCATGAACGACGTGCGCCGAGCCTTCTTGGGACCTTTTGCTCACAAAGAGGGGCCTACACATCAGTGGGTGTCCTACCAGGGTCGGGTACCCTACCCAAGACCTGGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016512:ENSRNOT00000066296:10
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(5.2=100)
A:
NA
C2:
PF0140314=Sema=FE(10.8=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:
TCCTTTTGTCCTCCCGAGACC
R:
GACACCCACTGATGTGTAGGC
Band lengths:
169-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]