BtaINT0130970 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62877834-62878502:-
Coord C1 exon
chr10:62878339-62878502
Coord A exon
chr10:62877946-62878338
Coord C2 exon
chr10:62877834-62877945
Length
393 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TAGCCCGTTTTTACTTGCAGATT
3' ss Score
8.59
Exon sequences
Seq C1 exon
GTAGCTAAGTGGACTCTCTGAGGAGGGGCTGCTCTGCCTTCACGTTGGCCCAACCATGAGGTTCTTCCTGCTCTGTGCCTACATGCTGCTGCTACTGATTTCCCAGTTGAGGGCAGTCAGCTTTCCTGAAGATGATGAACCCCTTAATACTGTTGACTATCACT
Seq A exon
GTAAGTAATCTAAAGAATACTCTTTTCTAAGAAGGAAGGGTTGTTTTGGTTTTAATTTTCTAAGCATATTCATTTTTAGAAAGAGGATTTTATGTCTTTAAAATGTTTTACATCCTCATTTATCCATAATCATTTCCTAGTGTCTGAAGAAAATGGGACAATTTAGTTAGGCACTTTTCTAAAGCAACCTATATATAGGTTATATGTTTTCAGTTAAAAAGAAAAAGACCATTTGGTGATACTCACCATCTCTTATTCATTCATATTCAAGACCTTAAGAAAAGAATTTAGTTAAAACCCTTCTACAACTAGTATATACAGCTAATCAATGCTGTATATCGATTCTTCAGCTCCGTAATCCTGACTGATGGTTTAGCCCGTTTTTACTTGCAG
Seq C2 exon
ATTCAAGGCAATATCCGGTTTTTAGAGGACGTCCTTCAGGCAATGAATCACAGCACAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(3.8=42.1)
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:
AAGTGGACTCTCTGAGGAGGG
R:
CTGCCAGCAATATAAAGTGTGTCT
Band lengths:
270-663
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development