BtaINT0130764 @ 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
chr22:50734908-50735293:-
Coord C1 exon
chr22:50735252-50735293
Coord A exon
chr22:50735066-50735251
Coord C2 exon
chr22:50734908-50735065
Length
186 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GCCCCTACCCCTGCCCACAGCAA
3' ss Score
8.13
Exon sequences
Seq C1 exon
GACCCAGCACCTGTTAAGACCATGACCATCTCTTCCAAGAGG
Seq A exon
GTGAGTTTAGGCGAGGTGGGCTGGGAGTGGGCATGGAGCCCACCTCCCCTTGGGGTCAAGCCCGTGGTAAAGAGAGATGGGGGATATTGAGGCACCGAACAGGAAGGGGAGGAGCCCAGCTCAGCTGGCTCCTAAGGAAAGCTGGCTGCCAAGAGGGAACTGACAAGCCCCTACCCCTGCCCACAG
Seq C2 exon
CAACAACTGTACGTGGCCTCAGCCGTGGGCGTCACACAGCTGAGCCTGCACCGCTGTCAGGCATATGGGGCCGCCTGTGCCGACTGCTGCCTCGCCCGGGACCCCTACTGCGCCTGGGATGGCCAAGCCTGTTCCCGCTACACAGCGTCCTCTAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:14
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(2.7=100)
A:
NA
C2:
PF0143720=PSI=PU(66.0=66.0)
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:
ACCCAGCACCTGTTAAGACCA
R:
TCTTAGAGGACGCTGTGTAGC
Band lengths:
198-384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]