BtaINT0130964 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62871881-62872971:-
Coord C1 exon
chr10:62872798-62872971
Coord A exon
chr10:62872022-62872797
Coord C2 exon
chr10:62871881-62872021
Length
776 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGT
5' ss Score
6.84
3' ss Seq
AAATGTCTCCCACAATATAGGTG
3' ss Score
5.21
Exon sequences
Seq C1 exon
GTACAGACTGACGGCCATCGCCGTCGACCATTCTGCCGGACCCCACCAGAACTACACAGTCATCTTTGTTGGCTCAGAAGCTGGCGTGGTGCTTAAAGTTTTGGCGAAGACCAGCCCTTTCTCTTTGAATGACAGCGTATTACTGGAAGAGATTGAAGCATACAACCATGCAAA
Seq A exon
GTAGGTGTATTATACCAGAACGCTTTTTGAGACTTCAGCGTCTGTTTCATCTAGTCATTTCCTTTCAGCCCGCTATATTAGCAGTGGTAGAAATGGAGAAGGCAATGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTACCTTACAGATCTATTTCAGGGTGCTGCATCCCTAACTATGCTACAGCTGGTTGCAGATAGACACACACACACACACACACACACACACACACACACACACACACACAACCACCATAATTCTTGCAACCACTGATATAAAAAATTATATGAACCATTAAAACAAACGAGATAGATGAGAGTAATGGAGCAAAGAAGACTAAGGAGAGATCTAGAAATAGTTAGCACAGGAAGATTAAAATGCATTAGAACATTATCCTTTTTCTTCCCTATAGCCTAACATGCTCTTCACAAGTGCAATTCCCTTCTATCATCAGAACAGGAAGCCAGTCTTTAAAAAACCCTTTGTCCAGCCTGAAATTTAACTAACCATGCAAAGCAGTAGAAGATGAATCACATAATTATCACATCCTAAACTGTGTACTTGCGTAGTTTGCTACTGAGAGTATTCCTTAACACCTCCCCAGCTCTCAGTAATTGCAAAAACCAAACCCCACTTGCCTCGCCTAGTTCCTATAGCTCTTGACTTACTAAACATCTACCTTGAAAATGTCTCCCACAATATAG
Seq C2 exon
GTGCAGTGCTGAAAATGAGGAGGACAGAAAGGTCATCTCATTACAGTTGGATAAAGACCATCATGCTTTATATGTGGCGTTCTCTAGCTGCGTTATCCGCATCCCCCTCAGTCGCTGTGAGCGTTATGGATCATGTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:13
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(13.6=100)
A:
NA
C2:
PF0140314=Sema=PD(1.4=12.5),PF0143720=PSI=PU(14.5=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACAGACTGACGGCCATCG
R:
ACATGATCCATAACGCTCACAGC
Band lengths:
310-1086
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development