HsaINT0147221 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50275012-50275459:+
Coord C1 exon
chr3:50275012-50275053
Coord A exon
chr3:50275054-50275301
Coord C2 exon
chr3:50275302-50275459
Length
248 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GAGCCCCTCGTGCCCCCTAGCAC
3' ss Score
4.99
Exon sequences
Seq C1 exon
GACTCGGCCGCTGTCACCAGCATGCAAATTTCTTCCAAGAGG
Seq A exon
GTGAGTGACCAGGATGGGGGTCGGGGTGGGATGGACTGAGCTTGTGCCTGGCGCGTCCCAAGCCTCTGGCCCCTTTTGGTAGTTTGCAGTCCCGGGTTTGAGTACAGGCTCTGGCTTTGTTAGACTGTGTGACCTGAGGCGTAAGACCTCAGTGTTCCCATCTGTCGAGTGGAAGAAGGGATCCCTGACCGATGGGAGGCAGGCGTGGGGTCGCCCTCGGTCAGCCCAGAGCCCCTCGTGCCCCCTAG
Seq C2 exon
CACCAGCTGTACGTAGCCTCGCGGAGCGCGGTGGCCCAGATCGCGTTGCACCGCTGCGCTGCCCACGGCCGCGTCTGCACCGAATGCTGTCTGGCGCGTGACCCCTACTGCGCCTGGGACGGGGTCGCGTGCACGCGCTTCCAGCCCAGTGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:13
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(8.4=100)
A:
NA
C2:
PF0143720=PSI=PU(54.7=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTCACCAGCATGCAAATTTCT
R:
CTTGGCACTGGGCTGGAAG
Band lengths:
188-436
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