BtaINT0130912 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020489 | SEMA6A
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:HGNC Symbol;Acc:HGNC:10738]
Coordinates
chr7:38762345-38762646:+
Coord C1 exon
chr7:38762345-38762485
Coord A exon
chr7:38762486-38762565
Coord C2 exon
chr7:38762566-38762646
Length
80 bp
Sequences
Splice sites
5' ss Seq
AAAGTACGT
5' ss Score
7.99
3' ss Seq
CAGTCATTCTCTTCCTGCAGAAC
3' ss Score
9.51
Exon sequences
Seq C1 exon
GTGCAGCTATGACGGAGTAGAAGACAAGAGGATCATGGGCATGCAGCTGGACAAAGCCAGCAGCTTCCTGTATGTTGCATTCTCCACTTGTGTGATCAAGGTTCCCCTTGGCCGGTGTGAGCGGCATGGCAAGTGTAAAAA
Seq A exon
GTACGTATTTGCCTCATTGATATGTTCACGGTGCTTAGGGAAGAGTCCTAGGTAAGCTCACAGTCATTCTCTTCCTGCAG
Seq C2 exon
AACCTGTATTGCTTCCAGAGACCCCTACTGTGGGTGGGTAAAGGAAGCAGGTGCGTGTGCCCATCTGTCGCCCAGCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020489:ENSBTAT00000043906:13
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:
PF0140314=Sema=PD(3.4=31.2),PF0143720=PSI=PU(13.4=18.8)
A:
NA
C2:
PF0143720=PSI=FE(40.3=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:
ACAAGAGGATCATGGGCATGC
R:
CTGCTTCCTTTACCCACCCAC
Band lengths:
168-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]