BtaINT0130709 @ 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
chr22:50658151-50658443:-
Coord C1 exon
chr22:50658374-50658443
Coord A exon
chr22:50658296-50658373
Coord C2 exon
chr22:50658151-50658295
Length
78 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTGACATCTTCACCTGCAGCAG
3' ss Score
7.91
Exon sequences
Seq C1 exon
AGGACGTGTTCCTGTTGTCCTCGAGAGATCGCTGGACCCCACTGCTCTATGCTGTCTTCTCCACATCCAG
Seq A exon
GTGAGGTGTGGGAGGCAGTGGGCAGGGTGGCCCAGGCTCCACTGGAGCCCTTCGCTCCACTGACATCTTCACCTGCAG
Seq C2 exon
CAGCATCTTCCAGGGTTCTGCCGTGTGCGTGTACAGCATGAATGATGTACGCCGGGCCTTCCTGGGACCCTTTGCACACAAGGAGGGGCCCATGCACCAGTGGGTGTCCTACCAGGGACGTGTCCCCTACCCCCGACCTGGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010138:ENSBTAT00000013382:9
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:
TGTTGTCCTCGAGAGATCGCT
R:
GGACACGTCCCTGGTAGGA
Band lengths:
183-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]