BtaINT0130957 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19722640-19723048:+
Coord C1 exon
chr3:19722640-19722730
Coord A exon
chr3:19722731-19722928
Coord C2 exon
chr3:19722929-19723048
Length
198 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
CACCCTACCCACCCCTCCAGAGG
3' ss Score
6.95
Exon sequences
Seq C1 exon
ATAACTTCGCTGCAGCAGGAGGGTGAGGAGCTGAGTGGGCAAGCTCGATGCCCCTTTGATGCCACCCAGTCCAACGTGGCCGTGTTTGCAG
Seq A exon
GTGTGCACCTGGGCATGTGAGAAGCAGGCATGTGGCTGCCATGTTAGCCCCTTTCTGAGTTTGGTCTTTCCTGCATGCTCCTGAATCAGGGGTGAGGTAGGGGCCAGGGTCAGGCCAAGGTAGGGGTGTGGGATGCCCAAGGAGAGCCAAGATACAGATCCCTGAGCCCCCCTGATGCCACCCTACCCACCCCTCCAG
Seq C2 exon
AGGGCAGCCTGTACTCAGCCACAGCTGCAGACTTCCAGGCCAGTGATGCTGTGGTTTACCGAAGCCTTGGGCCTCAGCCCCCGCTCCGCTCCGCCAAGTACGACTCCAAGTGGCTCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(7.1=100)
A:
NA
C2:
PF0140314=Sema=FE(9.4=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:
ATAACTTCGCTGCAGCAGGAG
R:
TCGGAGCCACTTGGAGTCGTA
Band lengths:
210-408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]