HsaINT1041208 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50273759-50274057:+
Coord C1 exon
chr3:50273759-50273828
Coord A exon
chr3:50273829-50273912
Coord C2 exon
chr3:50273913-50274057
Length
84 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GCCCTGGTCTTCGCCTCCAGCAG
3' ss Score
7.89
Exon sequences
Seq C1 exon
AGGATGTGTTTCTGTTGTCCTCGCGGGACCACCGGACCCCGCTGCTCTATGCCGTCTTCTCCACGTCCAG
Seq A exon
GTGAGGGGCAGGAGGTAGGGAGCGCCCGGGGCGGGCCGCTGGGCTCCACCCGGCCCCTCACCTCGCCCTGGTCTTCGCCTCCAG
Seq C2 exon
CAGCATCTTCCAGGGCTCTGCGGTGTGCGTGTACAGCATGAACGACGTGCGCCGGGCCTTCTTGGGACCCTTTGCACACAAGGAGGGGCCCATGCACCAGTGGGTGTCATACCAGGGTCGCGTCCCCTACCCGCGGCCAGGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:9
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(5.2=100)
A:
NA
C2:
PF0140314=Sema=PU(22.7=97.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTGTTGTCCTCGCGGGA
R:
CGCGACCCTGGTATGACAC
Band lengths:
183-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains