HsaINT0147219 @ hg19
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:HGNC Symbol;Acc:10724]
Coordinates
chr3:50311794-50312365:+
Coord C1 exon
chr3:50311794-50312013
Coord A exon
chr3:50312014-50312273
Coord C2 exon
chr3:50312274-50312365
Length
260 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
ACCCCTTCTCATCCCTGCAGACG
3' ss Score
12.17
Exon sequences
Seq C1 exon
TGCCCCAGCAAGACCTTTGGCACCTTCAGTTCCACCAAGGACTTCCCAGACGATGTCATCCAGTTTGCGCGGAACCACCCCCTCATGTACAACTCTGTCCTGCCCACTGGGGGGCGCCCTCTTTTCCTACAAGTTGGAGCCAATTACACCTTCACTCAAATTGCCGCGGACCGGGTTGCAGCCGCTGACGGACACTATGACGTCCTCTTCATTGGCACAG
Seq A exon
GTCAGGGTCCCTCCACAGCGACCCCCAGGCTCCCAGCCAGGCCCTGTGGGCTGCTGATGGAAGCTCTCCCTGTTCAGTCCCATCTCCACATCCTTTCCTGGGCTGTGTCTCCACCCTGTGGATGCTGCCCAACCCACACTCTTCCAGTCCACACTCTTCACAACCCAAACATGCTGAGGGTAGACGCCTCAAAGGCGAGGAGACACTAGCCCCAGCTGTCCGGGAGCACCAATGGTCATTACCCCTTCTCATCCCTGCAG
Seq C2 exon
ACGTTGGCACGGTGCTGAAGGTGATCTCGGTCCCCAAGGGCAGTAGGCCCAGCGCAGAGGGGCTGCTCCTGGAGGAGCTGCACGTGTTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171-SEMA3B:NM_001005914:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGGCACCTTCAGTTCCACC
R:
CTCAAACACGTGCAGCTCCTC
Band lengths:
297-557
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)