BtaINT0130963 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62872798-62873218:-
Coord C1 exon
chr10:62873063-62873218
Coord A exon
chr10:62872972-62873062
Coord C2 exon
chr10:62872798-62872971
Length
91 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TGATTCACCTCCTCTGGCAGGTA
3' ss Score
8.69
Exon sequences
Seq C1 exon
GCCTGGGTGTTGTGCAAAGCACGGTCTTGCGGAAGCATATAAAACCTCCATCGATTTCCCGGATGAAACCCTGTCATTCATCAAATCCCACCCCCTGATGGACTCGGCCGTCCCACCCATTGCCGACGAACCCTGGTTCACAAAGACTCGGATCAG
Seq A exon
GTAAGACTGGGCAGACACGCAGGCCCGCTCCCGTTCAGTAGTCCCCCTTCCTGTTGGCCCCCTGTCTAACCTGATTCACCTCCTCTGGCAG
Seq C2 exon
GTACAGACTGACGGCCATCGCCGTCGACCATTCTGCCGGACCCCACCAGAACTACACAGTCATCTTTGTTGGCTCAGAAGCTGGCGTGGTGCTTAAAGTTTTGGCGAAGACCAGCCCTTTCTCTTTGAATGACAGCGTATTACTGGAAGAGATTGAAGCATACAACCATGCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:12
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(12.2=100)
A:
NA
C2:
PF0140314=Sema=FE(13.6=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:
ACCTCCATCGATTTCCCGGAT
R:
ACTGTGTAGTTCTGGTGGGGT
Band lengths:
173-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development