BtaINT0130833 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001941 | SEMA4D
Description
Bos taurus sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D (SEMA4D), mRNA. [Source:RefSeq mRNA;Acc:NM_001098160]
Coordinates
chr8:90237593-90238034:+
Coord C1 exon
chr8:90237593-90237768
Coord A exon
chr8:90237769-90237877
Coord C2 exon
chr8:90237878-90238034
Length
109 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CGTCACCCCCTCCTCCCCAGGAA
3' ss Score
8.97
Exon sequences
Seq C1 exon
GGGGACCAGGGGGGCCTGAGGACCTTACAGAAGAAGTGGACCTCCTTCCTGAAGGCCAGGCTCATCTGCTCCCGGCCGGACAGCAACCTCGTCTTTAACGTGCTGCGGGATGTCTTCGTCCTCAGGTCTGCGGACCTGAAGGAACCCGTGTTCTACGGGGTCTTCACCCCGCAGCT
Seq A exon
GTGAGTGCTCCAGGCGGGCAGGGGTGGGGTGTTTTCACCGCACTTTCCTTCCCCCGACCCGTGCCCTGCCCCCCGCCTCAGGGCAGTCACGTCACCCCCTCCTCCCCAG
Seq C2 exon
GAACAACGTGGGGCTGTCGGCCGTGTGCGCCTACAACCTGTCCACGGCTGAGGCGGTCTTCTCCCGTGGGAAGTACATGCAGAGCGCCACGGTGGAGCAGTCCCACACCAAGTGGGTGCGCTACAACGGGGCTGTGCCCACGCCGCGGCCCGGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001941:ENSBTAT00000002525:10
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=0.038
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.4=100)
A:
NA
C2:
PF0140314=Sema=FE(12.0=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:
GGCCTGAGGACCTTACAGAAGA
R:
CTCTGCATGTACTTCCCACGG
Band lengths:
248-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]