BtaINT0130820 @ 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
chr11:2787231-2787695:-
Coord C1 exon
chr11:2787473-2787695
Coord A exon
chr11:2787344-2787472
Coord C2 exon
chr11:2787231-2787343
Length
129 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
GTTCCCCCCAACCCCTGCAGGAG
3' ss Score
8.29
Exon sequences
Seq C1 exon
TGCATCAACAACTGGCACCGGCGCCACGGCTACACCAGCTCCCTGGAGCTGCCGGACAACATCCTCAACTTCATCAAGAAGCACCCGCTGATGGAGGAGCAGGTGCGGCCTCGCTGGGGCCGCCCCCTGCTGGTGAAGAAGAACGCCAACCTCACCCACCTGGTGGCGGACCGCGTCACGGGGCTCGATGGGGCCACCTACACCGTGCTGTTCATCGGCACAG
Seq A exon
GTGGGTACGGGCGTGGCAGCTGGGGGCTAGGCGAAGGCCTGTGTGCCCGAAGCAGGGAGATCCAGAGACAGCCCCACCCCGGGACCCTCCTGCCCTTTTCTTGACACCTGTTCCCCCCAACCCCTGCAG
Seq C2 exon
GAGACGGCTGGCTTCTCAAGGCCGTGAGCCTGGGGCCCTGGGTTCACCTGATTGAGGAGCTGCAGCTGTTTGACCAGGAGCCTGTGGAGAGCCTGGTCCTGTCCCGGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021920:ENSBTAT00000029225:11
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(17.2=100)
A:
NA
C2:
PF0140314=Sema=FE(8.6=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:
GCCGGACAACATCCTCAACTT
R:
CTCCTGGTCAAACAGCTGCAG
Band lengths:
253-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development