BtaINT0130702 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010138 | SEMA3B
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr22:50660821-50661178:-
Coord C1 exon
chr22:50661021-50661178
Coord A exon
chr22:50660884-50661020
Coord C2 exon
chr22:50660821-50660883
Length
137 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCA
5' ss Score
3.41
3' ss Seq
CATCCCCACCCTCCCCATAGCTG
3' ss Score
10.36
Exon sequences
Seq C1 exon
AGCTCCAGGCCCAGCACGGTCTCCGGACCTTCAGGCTGGAGAGGACCTGCTGCTATGAAGCGCTGCTGCTCGATGAGGAACGTGGGCGCCTGTTTGTGGGCGCCGAGAACCACGTGGCCTCCCTCAGCCTGGACAACATTAGCAAGAGGGCCAAGAAG
Seq A exon
GTGCCAGAAACCCCACCACCACCCAGCCTCAGCACCAGCCCCCCAGGAAAGAGCCCCGGGGAGGTTGGGTCCCCTGAGTGGACACCCTCAGCTTAGAGACCGGGCCCTGTGTTCGCCCATCCCCACCCTCCCCATAG
Seq C2 exon
CTGGCCTGGCCGGCCCGTGTGGAATGGCGAGAGGAGTGCAACTGGGCCGGGAAGGACATTGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010138:ENSBTAT00000013382:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.080 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(19.1=64.2)
A:
NA
C2:
PF0140314=Sema=FE(11.2=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:
CAGGCCCAGCACGGTCTC
R:
AATGTCCTTCCCGGCCCAG
Band lengths:
213-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]