HsaINT0147473 @ hg19
Intron Retention
Gene
ENSG00000167680 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:10739]
Coordinates
chr19:4546228-4546481:-
Coord C1 exon
chr19:4546404-4546481
Coord A exon
chr19:4546287-4546403
Coord C2 exon
chr19:4546228-4546286
Length
117 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
GTGCCTCCTCTCCCCATTAGAGC
3' ss Score
7.6
Exon sequences
Seq C1 exon
GAACTGTATCGGCAGTCAGGACCCCTACTGCGGGTGGGCCCCCGACGGCTCCTGCATCTTCCTCAGCCCGGGCACCAG
Seq A exon
GTACTGCGGGAGAGGGAGGTGGGTGGAGGGTGTGTCAGACCCGCCCATGATCCCAGATCCCCCTGATCTCTGACTGTGAGAGGGGCCTCTGCTGACGGTGCCTCCTCTCCCCATTAG
Seq C2 exon
AGCCGCCTTTGAGCAGGACGTGTCCGGGGCCAGCACCTCAGGCTTAGGGGACTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167680-SEMA6B:NM_032108:14
Average complexity
IR-S
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:
PF0143720=PSI=FE(46.4=100)
A:
NA
C2:
PF0143720=PSI=FE(35.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGTATCGGCAGTCAGGACC
R:
CAGTCCCCTAAGCCTGAGGTG
Band lengths:
130-247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)