BtaINT0130704 @ 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
chr22:50660105-50660404:-
Coord C1 exon
chr22:50660285-50660404
Coord A exon
chr22:50660199-50660284
Coord C2 exon
chr22:50660105-50660198
Length
86 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
AACTCCCTGCTGCCTCTCAGGAG
3' ss Score
5.67
Exon sequences
Seq C1 exon
ACCGAGTGCATGAACTTCGTGAAGTTGCTCCATGCCTACAACCATACCCACTTGCTGGCCTGTGGCACAGGGGCCTTCCACCCAATCTGTGCGTTTGTGGAGGTGGGCCAGCGGCTGGAG
Seq A exon
GTAAGGCTGGAGCTGGTCAGGGAGGGAGGTAGGGAGAGTAAGGAAGGAGGAAGGGCCTGTACTAGTAACTCCCTGCTGCCTCTCAG
Seq C2 exon
GAGCCCATGCTCCGGCTGGACCCTCGAAGGCTGGAGGATGGCAAGGGCAAGAGTCCTTATGACCCCAGGCATCGGGCTGCCTCCGTGCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010138:ENSBTAT00000013382:4
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=0.406
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(21.9=100)
A:
NA
C2:
PF0140314=Sema=FE(17.4=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:
GTTGCTCCATGCCTACAACCA
R:
GCCTGGGGTCATAAGGACTCT
Band lengths:
167-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]