RnoINT0132823 @ rn6
Intron Retention
Gene
ENSRNOG00000016512 | Sema3b
Description
semaphorin 3B [Source:RGD Symbol;Acc:1310079]
Coordinates
chr8:116359195-116359479:-
Coord C1 exon
chr8:116359360-116359479
Coord A exon
chr8:116359289-116359359
Coord C2 exon
chr8:116359195-116359288
Length
71 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
AACAACTGCCCTACCCCCAGGAA
3' ss Score
8.09
Exon sequences
Seq C1 exon
ACGGAGTGCATGAACTTCGTGAAGCTGTTGCATGCCTACAACCACACCCACCTGCTGGCCTGCGGCACAGGGGCCTTCCACCCCACCTGTGCATTTGTGGAGGTGGGCCACCGGCTGGAG
Seq A exon
GTAAGACCAGGACGGAGGAGAGGCAGGAAGGGTGACAGACAACTTGGTATTAACAACTGCCCTACCCCCAG
Seq C2 exon
GAACCCATGCTCCGCCTGGACCTGAGGAAGCTCGAGGATGGCAAGGGAAAGAGTCCATATGACCCAAGGCACCGGGCTGCCTCGGTGCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016512:ENSRNOT00000066296:5
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=0.094
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.8=100)
A:
NA
C2:
PF0140314=Sema=FE(7.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGTGCATGAACTTCGTGA
R:
TCTTTCCCTTGCCATCCTCGA
Band lengths:
171-242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]