HsaINT0147218 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50273913-50274582:+
Coord C1 exon
chr3:50273913-50274057
Coord A exon
chr3:50274058-50274362
Coord C2 exon
chr3:50274363-50274582
Length
305 bp
Sequences
Splice sites
5' ss Seq
ATGGTTCGT
5' ss Score
6.1
3' ss Seq
TCCCTTTCCCCCACCCCCAGTGC
3' ss Score
9.88
Exon sequences
Seq C1 exon
CAGCATCTTCCAGGGCTCTGCGGTGTGCGTGTACAGCATGAACGACGTGCGCCGGGCCTTCTTGGGACCCTTTGCACACAAGGAGGGGCCCATGCACCAGTGGGTGTCATACCAGGGTCGCGTCCCCTACCCGCGGCCAGGCATG
Seq A exon
GTTCGTAGCCCAGGGACTTCTGCTACAACCCACTTCAAAGCCTCAAGGGTTTGAGAACTTGGCCTGGGGTCTTCTTGGTGAATGTGGTTTCTTCCTTTAGTTATGGGTGGGAAAACGTTTCCATCATAAGACAAGGCTTGTTTCCCGCCTCTGACTTCCTAGGGCAAGGCTGATCTCCTCTCTAATTCTCAGGGCAGGGTTCTGTCCCCATCCCCCTCCATGTTCCCAGAGGCTGGGCATGGAGGGCTGCCTATCAAGCCCCCATATCTATATCCCTGCTGTGCCTCCCTTTCCCCCACCCCCAG
Seq C2 exon
TGCCCCAGCAAGACCTTTGGCACCTTCAGTTCCACCAAGGACTTCCCAGACGATGTCATCCAGTTTGCGCGGAACCACCCCCTCATGTACAACTCTGTCCTGCCCACTGGGGGGCGCCCTCTTTTCCTACAAGTTGGAGCCAATTACACCTTCACTCAAATTGCCGCGGACCGGGTTGCAGCCGCTGACGGACACTATGACGTCCTCTTCATTGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:10
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(22.7=97.2)
A:
NA
C2:
PF0140314=Sema=FE(47.4=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:
GGTGTGCGTGTACAGCATGAA
R:
CTGTGCCAATGAAGAGGACGT
Band lengths:
344-649
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