HsaINT0147220 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50274843-50275053:+
Coord C1 exon
chr3:50274843-50274934
Coord A exon
chr3:50274935-50275011
Coord C2 exon
chr3:50275012-50275053
Length
77 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
TCGCCCCTCCTCCCTCTCAGGAC
3' ss Score
9.88
Exon sequences
Seq C1 exon
ACGTTGGCACGGTGCTGAAGGTGATCTCGGTCCCCAAGGGCAGTAGGCCCAGCGCAGAGGGGCTGCTCCTGGAGGAGCTGCACGTGTTTGAG
Seq A exon
GTGAGGCCTCACCCCCAGTCGCCCGGGACCCCCCCACCCCACTAAGCCCTGACCCCGTCGCCCCTCCTCCCTCTCAG
Seq C2 exon
GACTCGGCCGCTGTCACCAGCATGCAAATTTCTTCCAAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:12
Average complexity
IR
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=FE(19.5=100)
A:
NA
C2:
PF0140314=Sema=FE(8.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGGTGCTGAAGGTGATCTC
R:
CCTCTTGGAAGAAATTTGCATGCT
Band lengths:
127-204
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