BtaINT0130944 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19724492-19725048:+
Coord C1 exon
chr3:19724492-19724644
Coord A exon
chr3:19724645-19724874
Coord C2 exon
chr3:19724875-19725048
Length
230 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCA
5' ss Score
7.33
3' ss Seq
CCCGAGGCCTATTCCTCCAGGGC
3' ss Score
4.85
Exon sequences
Seq C1 exon
GCCCGGATCCTGTGCAGGAGTAGGTGTGGCTGCATTGTTCCCCTCTTCCCGAGATCTCCCTGATGATGTCCTGACCTTCATCAAGGCTCACCCACTCCTGGACCCTGCCGTGCCACCTGCCACCCATCAGCCTCTGCTCACCCTCACCAGCAG
Seq A exon
GTATCAGGCTGAAAAATCCTGACCACTGCCATCCGCCCCTCACCCACTCTCTTTTTCTGACCCCACAAGGTAAATCATATTAGTAGGAGGAAGAACCTATGAAAGTGGGAGGGACAGAGCTAAGAAGGAAACCCTGGGCTGGGGGAAGGGCAGAGAAGGGGTATCCAGGTCCTTGAAACACTCAAGCTTCCACTGGTCAGGCTGTCCTGACCCGAGGCCTATTCCTCCAG
Seq C2 exon
GGCCCTACTGACCCAGGTGGCTGTGGATGGCATGGCTGGTCCCTACAGTAACATCACAGTCCTGTTCCTTGGCTCCAATGATGGGACAGTGCTGAAGGTGCTGCCCCCAGGGGGGCAATCTGGGGGCTCTGAGCCCATTCTGTTGGAAGAGATCGATGCCTACAGCCCCTCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.102
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(13.7=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:
CTGCATTGTTCCCCTCTTCCC
R:
GGGCTGTAGGCATCGATCTCT
Band lengths:
292-522
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]