BtaINT0130768 @ 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
chr22:50742590-50742913:-
Coord C1 exon
chr22:50742753-50742913
Coord A exon
chr22:50742653-50742752
Coord C2 exon
chr22:50742590-50742652
Length
100 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGG
5' ss Score
4.89
3' ss Seq
CTGATCCCCCTCTCTGGCAGATC
3' ss Score
10.11
Exon sequences
Seq C1 exon
AGCTTAAGGCCACAGGCACCGCCCACTTCTTCAACTTCCTTCTCAACACAAGCGACTACCGAATCCTGTTCAAGGACGAGGACCACGACCGCATGTATGTGGGCAGCAAGGACTACGTGCTGTCCCTGGACCTGCATGACATCAACCGCGAGCCCCTCATT
Seq A exon
GTAAGGGCCAGGCCAGATGTGGGGCGGGGGATGCTGGGGGACGTGAGCCCCAGGGTGCGGGGCCCCTGCCGGCAGGCCCTCTGATCCCCCTCTCTGGCAG
Seq C2 exon
ATCCACTGGGCAGCCACCCCACAGCGCATTGAAGAGTGCGTGCTCTCAGGCAAGGATGGCAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:2
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=PU(7.2=63.0)
A:
NA
C2:
PF0140314=Sema=FE(4.2=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:
GGCACCGCCCACTTCTTC
R:
GTTGCCATCCTTGCCTGAGAG
Band lengths:
210-310
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]