BtaINT0130965 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62871708-62872021:-
Coord C1 exon
chr10:62871881-62872021
Coord A exon
chr10:62871786-62871880
Coord C2 exon
chr10:62871708-62871785
Length
95 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
TTCTGTCTGGTTGCATACAGGTC
3' ss Score
8.5
Exon sequences
Seq C1 exon
GTGCAGTGCTGAAAATGAGGAGGACAGAAAGGTCATCTCATTACAGTTGGATAAAGACCATCATGCTTTATATGTGGCGTTCTCTAGCTGCGTTATCCGCATCCCCCTCAGTCGCTGTGAGCGTTATGGATCATGTAAAAA
Seq A exon
GTAAGCTGATGTTTCTTTCCTTACCCTGGGTCTTTCAGGATCATGACCTTTGATAATGAGAAAATTCAGGTTACCTTCTGTCTGGTTGCATACAG
Seq C2 exon
GTCTTGTATTGCATCTCGAGACCCATACTGTGGCTGGTTAAGCCAAGGGGCCTGTGGTCGAGTGAGCCCAGCGATGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:14
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=PD(1.4=12.5),PF0143720=PSI=PU(14.5=18.8)
A:
NA
C2:
PF0143720=PSI=FE(41.9=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:
GCAGTGCTGAAAATGAGGAGGA
R:
ACAGTATGGGTCTCGAGATGCA
Band lengths:
170-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development