BtaALTD0019413-3/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62863669-62869293:-
Coord C1 exon
chr10:62869259-62869293
Coord A exon
chr10:62869126-62869258
Coord C2 exon
chr10:62863669-62867391
Length
133 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CTCCTGTGTGTCTGTTGCAGGTG
3' ss Score
13.09
Exon sequences
Seq C1 exon
ACATGGAGGTATCTTCATCTTCTGTTACCACAATG
Seq A exon
GCAAGTATCCCAGAAATTACACCTAAAGTGATTGATACCTGGAGACCTAAACTGACCAGCTCCCGGAAATTTGTAGTTCAAGATGACCCAAACACTTCTGATTTTACTGATCCTTTATCAGGTATCCCAAAGG
Seq C2 exon
GTGTACGGTGGGAAGTCCAGTCTGGAGAGGCCAACCAGATGGTCCACATGAATGTCCTCATCACCTGTGTCTTTGCAGCTTTTGTCTTGGGTGCGTTCATTGCAGGTGTGGCAGTCTACTGTTACCGTGACATGTTTGTTCGGAAAAACAGAAAGATCCATAAAGATGCAGAATCTGCCCAGTCATGCACAGACTCCAGTGGAAGTTTTGCCAAGCTGAATGGTCTCTTTGACAGCCCCGTCAAGGAATACCAACAGAATATTGATTCTCCCAAATTATATAGTAACCTGCTGACCAGTCGGAAAGAGCTGCCACCCAATGGAGATACAAAATCCATGGTCATGGACCATCGAGGCCAACCTCCTGAGTTGGCTGCTCTCCCCACTCCTGAGTCTACGCCTGTGCTTCACCAGAAGACCCTGCAGGCCATGAAGAGCCACTCAGAAAAGGCCCATGGCCATGGAGCTTCAAGGAAAGAAACCCCCCAGTTTTTTCCTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800-24-21,25-21,26-21-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.298 A=NA C2=0.793
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Skipping 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:
ACATGGAGGTATCTTCATCTTCTGT
R:
GCTTGGCAAAACTTCCACTGG
Band lengths:
251-384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development