HsaINT0147226 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50270127-50270495:+
Coord C1 exon
chr3:50270127-50270284
Coord A exon
chr3:50270285-50270432
Coord C2 exon
chr3:50270433-50270495
Length
148 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCA
5' ss Score
3.41
3' ss Seq
CTCCCCCAACCTCCCGATAGCTG
3' ss Score
8
Exon sequences
Seq C1 exon
AGCTCCAGGCCTGGCATGGTCTCCAGACTTTCAGCCTGGAGCGAACCTGCTGCTACCAGGCCTTGCTGGTGGATGAGGAGCGTGGACGCCTGTTTGTGGGTGCCGAGAACCATGTGGCCTCCCTCAACCTGGACAACATCAGCAAGCGGGCCAAGAAG
Seq A exon
GTGCCAGGGACTCCCAACCCCAGCACTCCCCAGGGAAGGAGCCCTGGGACCCCACTCCAGCCTGGAGAGACCCAGAGGAATGGCTCCCTGAGGTAGAGAATATCCCAAGTTCCTGACCTGTGTCCCCTCTCCCCCAACCTCCCGATAG
Seq C2 exon
CTGGCCTGGCCGGCCCCTGTGGAATGGCGAGAGGAGTGCAACTGGGCAGGGAAGGACATTGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:2
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=PU(21.2=64.2)
A:
NA
C2:
PF0140314=Sema=FE(12.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGCATGGTCTCCAGACTT
R:
CAATGTCCTTCCCTGCCCAG
Band lengths:
210-358
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