BtaINT0130922 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020489 | SEMA6A
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:HGNC Symbol;Acc:HGNC:10738]
Coordinates
chr7:38751361-38752267:+
Coord C1 exon
chr7:38751361-38751480
Coord A exon
chr7:38751481-38752178
Coord C2 exon
chr7:38752179-38752267
Length
698 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAC
5' ss Score
5.54
3' ss Seq
AAGTGCCCATTTGTCCACAGAAC
3' ss Score
7.88
Exon sequences
Seq C1 exon
ATGGAAAACTATACTCTGCTACAGTGACAGACTTCCTTGCCATTGATGCAGTCATCTACCGGAGTCTTGGAGACAGCCCAACCCTACGGACCGTCAAGCATGATTCAAAGTGGTTAAAAG
Seq A exon
GTGAACAAACAATTAAAAAAAGAAAGGAGGTGTGGTGGGGGAGATGTATATCTTGAAGGAGATTTAGCGTCTGAATGGTCCAGATTGTAGTTTCATTTTAGTAATGGCTTCTCACGGACAGGAAGGTGGAAATTGCATCTCTTGCCCCGAGTTGATTTATTACCTCCCCTTTTCACTTCCCATGAGTTTCTGGAGTATTATCAAAACTACCAACACCACTATAATAGAATACATTACATTCATCTTTCCTGCTTCAAGCTCTCATTTCAAAGTCCCACATAAAACCAACTAAACAAAACACTTCATTCATAGAAGGGAACGGGGAATTAGAGGTGGTGGGGAACAGGAAAAAAGCTGTTCACAACCCGAATGAGTCAAGGTTGACAAGGCAATGTGTACAAAATCTATTCTGTAGTATGAGCCTTGTATTGTAGAAAATAAAATTACAGAGATATGCAAAACTCATTTATTCTTCATTGTTCATTGCAACTGCTTCTGGAAGATTAAATCTGTAGGCTTAAATGCTTTTGGAAATCATTAAGCACTTGCATGTGTAAAGTCACTAGAAACAGTTAGTGTTAACCAAATGTCTAATGGCCCTACGATTTTATTTCATAACATGTCTTTGGTTGCAACTGATTGCAGTTCTTTTCACTCTGTGTGACACGCCCCCAATTAAAGTGCCCATTTGTCCACAG
Seq C2 exon
AACCGTATTTTGTCCAAGCGGTAGATTATGGAGACTACATCTACTTCTTCTTTAGGGAAATAGCGGTGGAGTACAACAGCATGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020489:ENSBTAT00000043906:7
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(9.2=100)
A:
NA
C2:
PF0140314=Sema=FE(6.7=100)
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:
TGGAAAACTATACTCTGCTACAGTGA
R:
TTCCCATGCTGTTGTACTCCAC
Band lengths:
206-904
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]