HsaINT0147224 @ hg19
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:HGNC Symbol;Acc:10724]
Coordinates
chr3:50313136-50314572:+
Coord C1 exon
chr3:50313136-50313275
Coord A exon
chr3:50313276-50313732
Coord C2 exon
chr3:50313733-50314572
Length
457 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACGCTGCCCTCTGCCCGCAGGTG
3' ss Score
13.34
Exon sequences
Seq C1 exon
ACTCGTCTCGTCCCGCGCTGCTGGAACACAAGGTGTTCGGCGTGGAGGGCAGCAGCGCCTTTCTGGAGTGTGAGCCCCGCTCGCTGCAGGCGCGCGTGGAGTGGACTTTCCAGCGCGCAGGGGTGACAGCCCACACCCAG
Seq A exon
GTGAGCCTTACTCCGCCCTCCCCGCCAGGCTCCTGTCCCACCCCCTGCATCCAGGAGAGGCCCCGCCCTACCCAACGAAGCCCCGTCCAACCAGACCCACTCCCCGCCCTGTCCAGTTTGGTCCCTCACCTGCACTCCACAAGCTGCTGAGGCCCCATTGCGTCCAACGGGGCTCCCGACCCGCCTCCCCTGAATCAAGGAGAAGACCCGCCCTCGACCCTCCCATTAAGGTCCCTGACCACCCCCCACCAAGTTCATGTAAACCCCGCCTCTTTCGGATTCTCCCTTGAAGACCACCAGCTCCCAAACACTCAGCCTTAAAATGTGCGCCTGCGGGCACCCCTTTCCCGCTCCACCTCGGCTCCCAATGACTCTTTGCTTCTTCCGTCGCGTGCTAGGGCCCGGAAGCCCTGTTCCCGGCCCGACACCCCCGCCTCACGCTGCCCTCTGCCCGCAG
Seq C2 exon
GTGCTGGCAGAGGAGCGCACCGAGCGCACCGCCCGGGGACTACTGCTGCGCAGGCTGCGGCGCCGGGACTCGGGCGTGTACTTGTGCGCCGCCGTCGAGCAGGGCTTTACGCAACCGCTGCGTCGCCTGTCGCTGCACGTGTTGAGTGCTACGCAGGCCGAACGACTGGCGCGGGCCGAGGAGGCTGCGCCCGCCGCGCCGCCGGGCCCCAAACTCTGGTACCGGGACTTTCTGCAGCTGGTGGAGCCGGGCGGAGGTGGCAGCGCGAACTCCCTGCGCATGTGCCGCCCGCAGCCTGCGCTGCAGTCACTGCCCCTGGAGTCGCGGAGAAAGGGCCGTAACCGGAGGACCCACGCCCCTGAGCCTCGCGCTGAGCGGGGGCCGCGCAGCGCAACGCACTGGTGACCAGACTGTCCCCACGCCGGGAACCAAGCAGGAGACGACAGGCGAGAGAGGAGCCAGACAGACCCTGAAAAGAAGGACGGGTTGGGGCCGGGCACATTGGGGGTCACCGGCCGATGGAGACACCAACCGACAGGCCCTGGCTGAGGGCAGCTGCGCGGGCTTATTTATTAACAGGATAACCCTTGAATGTAGCAGCCCCGGGAGGGCGGCACAGGTCGGGCGCAGGATTCAGCCGGAGGGAAGGGACGGGGAAGCCGAGCTCCAGAGCAACGACCAGGGCCGAGGAGGTGCCTGGAGTGCCCACCCTGGGAGACAGACCCCACCTCCTTGGGTAGTGAGCAGTGAGCAGAAAGCTGTGAACAGGCTGGGCTGCTGGAGGTGGGGCGAGGCAGGCCGACTGTACTAAAGTAACGCAATAAACGCATTATCAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171-SEMA3B:NM_001005914:17
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:
CAAGGTGTTCGGCGTGGAG
R:
CTCCACCAGCTGCAGAAAGTC
Band lengths:
358-815
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)