BtaINT0130831 @ 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
chr11:2787793-2788399:-
Coord C1 exon
chr11:2788224-2788399
Coord A exon
chr11:2787938-2788223
Coord C2 exon
chr11:2787793-2787937
Length
286 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TCCCTCCCTTGCTGTGACAGGGG
3' ss Score
8.55
Exon sequences
Seq C1 exon
GGCGACGTGGGGGGCGCGCGGACGCTGCAGAGGAAGTGGACCACGTTTCTGAAGGCACGGCTGGTGTGCTCCGCGCCCGACTGGCAGCTCTACTTCAACCGGCTGCAGGCGCTACACACGCTCCAGGATGCCTCCTGGCACAACACCACCTTCTTCGGGGTTTTTCGGGCGCGGTG
Seq A exon
GTGAGTTGGCTAGGAGCCCTTGGGGGTGGGGAGGAGCGGGTCTGTGGGTTAGGGATGGTTGATGGGGCAGGCCTCTGGGGGAGGTCCTGGGGGTCCAGGATGATGTTGGGCTCCCGCCCTTTTCACCACCCCTCCGTGAGAGGTGCCCCCAGTGGTGCTTTGAGCTGCCACCACATCACACGTGGCCATGGCCTTCTTGTGCCTGTGGGCCCTCCCTTTCTGCTGCACGCCCTGAGCTGTGGGCACCCCAGCTCTGACCCTTGGGGTCCCTCCCTTGCTGTGACAG
Seq C2 exon
GGGCGACATGGACCTGTCAGCAGTGTGCGAGTACCAGTTGGAGGAGATCCAGAAGGTGTTCGAGGGGCCCTACAAGGAGTACCACGAGCAGGCCCAGAAGTGGGGCCGCTACACTGACCCTGTCCCTAGCCCGCGGCCCGGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021920:ENSBTAT00000029225:9
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=0.082
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.5=100)
A:
NA
C2:
PF0140314=Sema=FE(11.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGACGCTGCAGAGGAA
R:
CGGGCTAGGGACAGGGTC
Band lengths:
292-578
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development