BtaINT0130967 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62870770-62871248:-
Coord C1 exon
chr10:62871187-62871248
Coord A exon
chr10:62870827-62871186
Coord C2 exon
chr10:62870770-62870826
Length
360 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
TGTTCCTTTAATTCTTTTAGAAA
3' ss Score
8.3
Exon sequences
Seq C1 exon
CGCTGGAGGATTTGAACAAGACACAGAATATGGCAACACGGCCCATCTAGGGGACTGCCACG
Seq A exon
GTAAGACCGAATCTTCCTTTCCCTCCTGGCGCTTCTTTTGGATCACATTTGCACGTGAACATTGTTTTATAATCAGCCTTATATAATGACTCAGTACACATGCCACCTAGCATTTAACTTGAACTTCGCAAAAGCTGAGCTGTTTGATCATGGGGATAAGTTAGAGAAGAATCTTACTTTTTTTTTTTTACCTTCGCCATTTGCAATTCCATAGGAAATCTAGAGAAAGGTAGTCTAACCAGTAGGTTCATTTTTTAATTTATAGTCCTTTCTTTTGACTTTTTGAGTTAATGGAATTCGTAAATTTTTGCTTTCTTTTGGTTACTTCTTACTGATTACTTGTTCCTTTAATTCTTTTAG
Seq C2 exon
AAATTTTGCCTACTTCAACTACACCAGATTACAAAATATTTGGCGGTCCAACATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:16
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=0.100
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(33.9=100)
A:
NA
C2:
PF0143720=PSI=PD(8.1=25.0)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development