HsaINT0147233 @ hg19
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:HGNC Symbol;Acc:10724]
Coordinates
chr3:50311190-50311488:+
Coord C1 exon
chr3:50311190-50311259
Coord A exon
chr3:50311260-50311343
Coord C2 exon
chr3:50311344-50311488
Length
84 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GCCCTGGTCTTCGCCTCCAGCAG
3' ss Score
7.89
Exon sequences
Seq C1 exon
AGGATGTGTTTCTGTTGTCCTCGCGGGACCACCGGACCCCGCTGCTCTATGCCGTCTTCTCCACGTCCAG
Seq A exon
GTGAGGGGCAGGAGGTAGGGAGCGCCCGGGGCGGGCCGCTGGGCTCCACCCGGCCCCTCACCTCGCCCTGGTCTTCGCCTCCAG
Seq C2 exon
CAGCATCTTCCAGGGCTCTGCGGTGTGCGTGTACAGCATGAACGACGTGCGCCGGGCCTTCTTGGGACCCTTTGCACACAAGGAGGGGCCCATGCACCAGTGGGTGTCATACCAGGGTCGCGTCCCCTACCCGCGGCCAGGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171-SEMA3B:NM_004636:10
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTGTTGTCCTCGCGGGA
R:
CGCGACCCTGGTATGACAC
Band lengths:
183-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)