HsaINT0147221 @ hg19
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:HGNC Symbol;Acc:10724]
Coordinates
chr3:50312443-50312890:+
Coord C1 exon
chr3:50312443-50312484
Coord A exon
chr3:50312485-50312732
Coord C2 exon
chr3:50312733-50312890
Length
248 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GAGCCCCTCGTGCCCCCTAGCAC
3' ss Score
4.99
Exon sequences
Seq C1 exon
GACTCGGCCGCTGTCACCAGCATGCAAATTTCTTCCAAGAGG
Seq A exon
GTGAGTGACCAGGATGGGGGTCGGGGTGGGATGGACTGAGCTTGTGCCTGGCGCGTCCCAAGCCTCTGGCCCCTTTTGGTAGTTTGCAGTCCCGGGTTTGAGTACAGGCTCTGGCTTTGTTAGACTGTGTGACCTGAGGCGTAAGACCTCAGTGTTCCCATCTGTCGAGTGGAAGAAGGGATCCCTGACCGATGGGAGGCAGGCGTGGGGTCGCCCTCGGTCAGCCCAGAGCCCCTCGTGCCCCCTAG
Seq C2 exon
CACCAGCTGTACGTAGCCTCGCGGAGCGCGGTGGCCCAGATCGCGTTGCACCGCTGCGCTGCCCACGGCCGCGTCTGCACCGAATGCTGTCTGGCGCGTGACCCCTACTGCGCCTGGGACGGGGTCGCGTGCACGCGCTTCCAGCCCAGTGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171-SEMA3B:NM_001005914:14
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:
CTGTCACCAGCATGCAAATTTCT
R:
CTTGGCACTGGGCTGGAAG
Band lengths:
188-436
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)