HsaINT0147223 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50275560-50275844:+
Coord C1 exon
chr3:50275560-50275615
Coord A exon
chr3:50275616-50275704
Coord C2 exon
chr3:50275705-50275844
Length
89 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GACTTTCTTCTCGCCCCAAGACT
3' ss Score
5.31
Exon sequences
Seq C1 exon
GCGGTTCCGGCGGCAAGACGTAAGGAATGGCGACCCCAGCACGTTGTGCTCCGGAG
Seq A exon
GTGAGTGCCCCAGCTGCCCCTACCCTCAGCCCCAGAAGACGCCCCACCTGCCCTGCCTTGCCTAAATCTGACTTTCTTCTCGCCCCAAG
Seq C2 exon
ACTCGTCTCGTCCCGCGCTGCTGGAACACAAGGTGTTCGGCGTGGAGGGCAGCAGCGCCTTTCTGGAGTGTGAGCCCCGCTCGCTGCAGGCGCGCGTGGAGTGGACTTTCCAGCGCGCAGGGGTGACAGCCCACACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(29.7=100),PF0768612=V-set=PU(12.1=65.0)
A:
NA
C2:
PF0143720=PSI=PD(14.1=19.1),PF0768612=V-set=FE(45.5=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:
AAGACGTAAGGAATGGCGACC
R:
CTGGGTGTGGGCTGTCAC
Band lengths:
182-271
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