BtaINT0130822 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021920 | SEMA4C
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:HGNC Symbol;Acc:HGNC:10731]
Coordinates
chr11:2785947-2786264:-
Coord C1 exon
chr11:2786107-2786264
Coord A exon
chr11:2786018-2786106
Coord C2 exon
chr11:2785947-2786017
Length
89 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
GATCCCTCTCCCCCCACCAGGTC
3' ss Score
10.32
Exon sequences
Seq C1 exon
AAGCTGCTCTTCGCGGGCTCCCGCTCCCAGCTGGTGCAGCTGCCCCCAGCCGACTGCATGAAGTACCGCTCCTGTGCCGACTGTGTGCTCGCCCGGGACCCCTACTGTGCCTGGAACGCCAACAGCAGCCGCTGCGTGGCTGTGGGCGGTCACTCCGG
Seq A exon
GTGAGGGGGGCTTCTGCGTGTGCGGGGACCAGCGGGGAGAGGAGGGTGGCAGGACCTGGGACGCTGATGGATCCCTCTCCCCCCACCAG
Seq C2 exon
GTCCCTGCTGATCCAGCACGTGACGGTCTCGGATACCTCAAGCATCTGTAATTTCCGGGGCAGTAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021920:ENSBTAT00000029225:13
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:
PF0143720=PSI=PU(60.3=66.0)
A:
NA
C2:
PF0143720=PSI=PD(37.9=88.0),PF138951=Ig_2=PU(1.3=4.0)
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:
GACTGCATGAAGTACCGCTCC
R:
TGCCCCGGAAATTACAGATGC
Band lengths:
169-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development