BtaINT0130972 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62877036-62877269:-
Coord C1 exon
chr10:62877209-62877269
Coord A exon
chr10:62877099-62877208
Coord C2 exon
chr10:62877036-62877098
Length
110 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTTTTGCTCGATTGATACAGAAA
3' ss Score
4.21
Exon sequences
Seq C1 exon
GGATCAAGTTTATACAGTAAACTTAAATGAAATCCCCAAAACAGAAGTAATACCAAACAAG
Seq A exon
GTGAGCAACTGTAGTTGGCAAATTTATTTGCATTCCCTTAGAACTTGGGTAATGTCCCTCTCCCCTCAATATTTAAAATATTGAACTTTGGTTTTGCTCGATTGATACAG
Seq C2 exon
AAACTGACATGGCGGTCAAGACAACAGGATCGAGAAAACTGTGCTATGAAAGGCAAGCATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:4
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=0.238
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(4.7=100)
A:
NA
C2:
PF0140314=Sema=FE(4.7=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:
ACAGTAAACTTAAATGAAATCCCCAA
R:
TGCTTGCCTTTCATAGCACAGT
Band lengths:
107-217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development