BtaINT0130766 @ 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
chr22:50734244-50734705:-
Coord C1 exon
chr22:50734638-50734705
Coord A exon
chr22:50734378-50734637
Coord C2 exon
chr22:50734244-50734377
Length
260 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GGCACCCTCTTGCTCTGCAGCCA
3' ss Score
7.47
Exon sequences
Seq C1 exon
GCGGAGCCGCCGGCAGGATGTCCGGCACGGGAACCCCATCCGGCAGTGCCGTGGGTTCAATTCCAATG
Seq A exon
GTGAGTGTGCTGTGTCTCATTACCACCACGCGGCCGCAGAGCCGGTCACGGGGCCCGCACTGCACAGACCCTCCCATGGTCCGTGGAGGTGAGGGGTTTTGGAGAAGGGATGTCCCTGGCCACCCCCTCCAGGAGTGGATGCCTGAGGGCACAGCCCTGCCTGTGTGTGTGGGGGTGTGTGTGGCTGTGTGTGCCCCCCGCCAGCCCACGGTCTGCCCAGAGGCGGTGCTGCTCTCACGTGGCACCCTCTTGCTCTGCAG
Seq C2 exon
CCAATAAGAACGCCGTGGAGTCTGTGCAGTACGGTGTGGCAGGGAGCACAGCCTTCCTTGAGTGCCAGCCCCGCTCGCCCCAGGCTACCGTGAAGTGGCTGTTCCAGCGAGATCCCAGTGACCGGCGCCGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(32.1=70.8)
A:
NA
C2:
PF0768612=V-set=PU(46.7=93.3)
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:
GAACCCCATCCGGCAGTG
R:
GCCGGTCACTGGGATCTCG
Band lengths:
164-424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]