BtaINT0130976 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62874730-62875609:-
Coord C1 exon
chr10:62875490-62875609
Coord A exon
chr10:62874819-62875489
Coord C2 exon
chr10:62874730-62874818
Length
671 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCT
5' ss Score
8.49
3' ss Seq
GTTCTCACTTTCTCTTTCAGAGC
3' ss Score
11.83
Exon sequences
Seq C1 exon
ATGGGAAGCTGTATTCTGCCACAGTGGCTGACTTCTTGGCCAGTGATGCTGTTATTTATCGAAGCATGGGTGATGGATCTGCTCTTCGTACAATAAAATATGATTCCAAATGGATCAAAG
Seq A exon
GTACCTTTGAAGAGCAGTATTGCCAGGGGTGGCAGGATGGGTACATGGGAACAGGAGCCCTGGCATTGGAAAGTTCAGTGCATGACTTTATATTGTTAATTTAGAGCCCAGTACAAGCTGCCTTGGTTGGCTGCATTAGTGGGAAATGAGGAGACCAGTAGCTATGTCTAGAAAGTAGATTTCTATCTTAGGTGACCTCAAAAAAAAAAAAAAAATCACCATTCTGTGTACCATTTGCCTAACTAAATGCACGCACTACTCCTTGCCCACTTCCTTCTAATTATCCTGGAAAGTTTAACCCTGGGAACTGTTAGTTCATATCTTCAGAGTTATTTTGTTCTTTGGAGTCTAGAAATCAAGATTTTTAATTTTCAACATAAAAAGTTTCCTTTACTAGCTAAATAGGTTAATGAATAAATCTGTTGAAACAAAGACCTTTGCTGTAGTTCAGTTCCCTGTAGGCTTTTTCTAGTCCATTAGCTAACATTAAAGACTCTGGGTTCCCTAAATCTTCAACATACCCATAATGGGACTCCAGAAACTTGGTGGCATATCAAAGTTCTTGGCTTGAAAGTAGCAGTGTGATGTCTGTCAGTCATGCCTAGCAGTCGGACTATGATGCTAATTGAATTACCCTTCAGGAACCAGTTTGTTCTCACTTTCTCTTTCAG
Seq C2 exon
AGCCACACTTTCTGCATGCTATAGAATACGGAAACTACGTCTATTTCTTCTTTCGAGAAATTGCTGTAGAACATAACAACTTAGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:8
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(9.4=100)
A:
NA
C2:
PF0140314=Sema=FE(6.8=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:
TGGGAAGCTGTATTCTGCCAC
R:
TGCCTAAGTTGTTATGTTCTACAGCA
Band lengths:
206-877
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development