HsaINT0147336 @ hg19
Intron Retention
Gene
ENSG00000185033 | SEMA4B
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:HGNC Symbol;Acc:10730]
Coordinates
chr15:90768514-90769059:+
Coord C1 exon
chr15:90768514-90768629
Coord A exon
chr15:90768630-90768892
Coord C2 exon
chr15:90768893-90769059
Length
263 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
CCCCGTGTCTGGCTGTGCAGGGG
3' ss Score
6.89
Exon sequences
Seq C1 exon
GTGACGGCCGGCTCCACAAGGCAGTGAGCGTGGGCCCCCGGGTGCACATCATTGAGGAGCTGCAGATCTTCTCATCGGGACAGCCCGTGCAGAATCTGCTCCTGGACACCCACAGG
Seq A exon
GTGAGCAGGCCAACGAGGAATCCTGGCAGGGTACTTGGGGGGTGCCCTCCATTAGCACCAAGCAGTCCCCACCCAGCTTCTCCTCCCTTGCCTCAGGAGGATGGAAAGATAAAGGATCCAGTCATGAACTATTAGAAAGTGGGGTCGCCTGTTACGTAACAGGCCTCTTGGGGGTGGCTCTGGGAGGCATACAAGCCGGGTGGCCATGGGTGATGGCCCTGGCTGCCCATGCCCGCTTCTCATCCCCGTGTCTGGCTGTGCAG
Seq C2 exon
GGGCTGCTGTATGCGGCCTCACACTCGGGCGTAGTCCAGGTGCCCATGGCCAACTGCAGCCTGTACAGGAGCTGTGGGGACTGCCTCCTCGCCCGGGACCCCTACTGTGCTTGGAGCGGCTCCAGCTGCAAGCACGTCAGCCTCTACCAGCCTCAGCTGGCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000185033-SEMA4B:NM_020210:12
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:
PF0140314=Sema=PD(52.0=78.0)
A:
NA
C2:
PF0140314=Sema=PD(0.1=0.0),PF0143720=PSI=PU(67.3=66.1)
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:
GCTCCACAAGGCAGTGAGC
R:
CTGGTAGAGGCTGACGTGCTT
Band lengths:
256-519
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)