BtaINT0130954 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19721680-19721956:+
Coord C1 exon
chr3:19721680-19721743
Coord A exon
chr3:19721744-19721899
Coord C2 exon
chr3:19721900-19721956
Length
156 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTTCTACTTTTCCCTCCAGTAT
3' ss Score
9.15
Exon sequences
Seq C1 exon
GGATCACGTTTTCTCCTTTGATCTTCAAGCCCAAGAAGAAGGGGAGAGGCTCATGCCCAACAAG
Seq A exon
GTGAGGGGCTGTGTGGGAGGAGGTTGAGGCATGGAGATGAGGCTGGAAAGGTCTAACGGCGATCCAGGGGGTGGGAAGAAGACTCCAAAAGGGAACCACAATGTGCGGTGGGTCCAGGCTGTGCCACGATTTTCCCTCTTCTACTTTTCCCTCCAG
Seq C2 exon
TATCTAACATGGAGGAGCCAAGACGTGGAGAACTGTGCCGTGCGGGGCAAGCTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:4
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(5.0=100)
A:
NA
C2:
PF0140314=Sema=FE(4.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCACGTTTTCTCCTTTGATCT
R:
CACGGCACAGTTCTCCACG
Band lengths:
106-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]