HsaINT0147468 @ hg19
Intron Retention
Gene
ENSG00000167680 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:10739]
Coordinates
chr19:4558038-4558503:-
Coord C1 exon
chr19:4558349-4558503
Coord A exon
chr19:4558162-4558348
Coord C2 exon
chr19:4558038-4558161
Length
187 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
CTCTCCACCCCCTCACTCAGACC
3' ss Score
6.32
Exon sequences
Seq C1 exon
AGGCGTCACCTCCTCCTGTCGCCTGGCCCTCGCCATGCAGACCCCGCGAGCGTCCCCTCCCCGCCCGGCCCTGCTGCTTCTGCTGCTGCTACTGGGGGGCGCCCACGGCCTCTTTCCTGAGGAGCCGCCGCCGCTTAGCGTGGCCCCCAGGGACT
Seq A exon
GTGAGTCTGGGGGTGTCTTTGGGCGGGGGTGGAGTCCCGTGGGAGTATCTGGGTTCCCAGTTGGGTCTGCTGCCCCCACTGGGGGACTCAAGCAGTCCAGGAGCCACCCCTAGAAGGGGCATGACCTCAGGCCACCCTCTCTTCACCCCCAGCCCTTGCTCACACCCCTCTCCACCCCCTCACTCAG
Seq C2 exon
ACCTGAACCACTATCCCGTGTTTGTGGGCAGCGGGCCCGGACGCCTGACCCCCGCAGAAGGTGCTGACGACCTCAACATCCAGCGAGTCCTGCGGGTCAACAGGACGCTGTTCATTGGGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167680-SEMA6B:NM_032108:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.171 A=NA C2=0.048
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(4.0=40.5)
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:
GGCGTCACCTCCTCCTGT
R:
CAGGACTCGCTGGATGTTGAG
Band lengths:
246-433
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)