BtaINT0130947 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19725738-19725997:+
Coord C1 exon
chr3:19725738-19725815
Coord A exon
chr3:19725816-19725941
Coord C2 exon
chr3:19725942-19725997
Length
126 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CCACCTCCATTTCCTCCTAGGAT
3' ss Score
9.14
Exon sequences
Seq C1 exon
GAGCTGTCTGGCTTCTCAGGACCCATACTGTGGATGGGACAGCTCCAGAGGCTGCGTGGATATCAGGGCACCTGGTGG
Seq A exon
GTAAGTGAGGGGCTCCTGGATCTCCTGAGGAAAAAGCTCCCCACTACTAAGAGAGGAGGCTGAGAGCTAGGGTGGGGGAGGGGACAAGAGGTATACCTGCACTGAGCCACCTCCATTTCCTCCTAG
Seq C2 exon
GATTGATGTGGATCCAACTGGTAACCAGGAATCCATGGAGCATGATGACTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.148 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(41.9=100)
A:
NA
C2:
PF0143720=PSI=FE(30.6=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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCTGTCTGGCTTCTCAGGA
R:
TGGCAGTCATCATGCTCCATG
Band lengths:
132-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]