BtaINT0130700 @ 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
chr22:50656389-50656676:-
Coord C1 exon
chr22:50656621-50656676
Coord A exon
chr22:50656529-50656620
Coord C2 exon
chr22:50656389-50656528
Length
92 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
GACATTCCCTTTGCCCCCAGACT
3' ss Score
9.32
Exon sequences
Seq C1 exon
GCGGTTCCGACGGCAGGACGTAAGGAACGGCGACCCCAGCACACTGTGTTCCGGGG
Seq A exon
GTGAGTGTCTCAGCTGCTCTCATCCCTCAGCGCTTAAAGACTGCCCCACCCTGTCCTGCTTTGCCTGAATCTGACATTCCCTTTGCCCCCAG
Seq C2 exon
ACTCATCCCACCCTGTGCTGCTGGAGCAGAAGGTGCTGGGTGTGGAGGGAGGTAGCGCCTTCCTGGAGTGTGAGGCCCGCTCGCTGCAGGCGCACGTGGAGTGGACCTTCCAGCGCGCGGGGGAGTCGGCCTACACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010138:ENSBTAT00000013382:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=0.043
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(29.2=100),PF0768612=V-set=PU(11.2=60.0)
A:
NA
C2:
PF0143720=PSI=PD(15.4=21.3),PF0768612=V-set=FE(43.0=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:
TAAGGAACGGCGACCCCAG
R:
CTGAGTGTAGGCCGACTCCC
Band lengths:
176-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]