BtaINT0130760 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018307 | SEMA3F
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:HGNC Symbol;Acc:HGNC:10728]
Coordinates
chr22:50737217-50737596:-
Coord C1 exon
chr22:50737527-50737596
Coord A exon
chr22:50737362-50737526
Coord C2 exon
chr22:50737217-50737361
Length
165 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGG
5' ss Score
5.5
3' ss Seq
GCAGCCTGCCCTGCCCGCAGCTC
3' ss Score
7.47
Exon sequences
Seq C1 exon
AGGATGTGTTTGTCCAGCAGACCCAGGATGTGAGGAACCCAGTCATCTACGCTGTCTTCACCTCCTCGGG
Seq A exon
GTGAGGCTAAGGCCAGGGCCAGCAGTAGCAGCGGGTGGCAGTTTGAGGGGCTATGACTTGTGGAGGACCCCATCCTGGTGGGGAGCTGTGGGCGAAAGCAGGCTGGGGAGGGGCCCTGGGCCAAGGGTCTGCCCCACCCACAGCAGCAGCCTGCCCTGCCCGCAG
Seq C2 exon
CTCTGTGTTCCGAGGCTCTGCCGTGTGTGTCTACTCCATGGCTGACATCCGCATGGTCTTCAATGGGCCCTTTGCCCACAAGGAGGGCCCCAACTACCAGTGGATGCCCTTCTCAGGAAAGATGCCCTACCCACGGCCCGGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:10
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=0.041
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(4.9=100)
A:
NA
C2:
PF0140314=Sema=FE(10.1=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:
ATGTGTTTGTCCAGCAGACCC
R:
CGTGGGTAGGGCATCTTTCCT
Band lengths:
202-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]