HsaINT0147224 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50275705-50277179:+
Coord C1 exon
chr3:50275705-50275844
Coord A exon
chr3:50275845-50276301
Coord C2 exon
chr3:50276302-50277179
Length
457 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACGCTGCCCTCTGCCCGCAGGTG
3' ss Score
13.34
Exon sequences
Seq C1 exon
ACTCGTCTCGTCCCGCGCTGCTGGAACACAAGGTGTTCGGCGTGGAGGGCAGCAGCGCCTTTCTGGAGTGTGAGCCCCGCTCGCTGCAGGCGCGCGTGGAGTGGACTTTCCAGCGCGCAGGGGTGACAGCCCACACCCAG
Seq A exon
GTGAGCCTTACTCCGCCCTCCCCGCCAGGCTCCTGTCCCACCCCCTGCATCCAGGAGAGGCCCCGCCCTACCCAACGAAGCCCCGTCCAACCAGACCCACTCCCCGCCCTGTCCAGTTTGGTCCCTCACCTGCACTCCACAAGCTGCTGAGGCCCCATTGCGTCCAACGGGGCTCCCGACCCGCCTCCCCTGAATCAAGGAGAAGACCCGCCCTCGACCCTCCCATTAAGGTCCCTGACCACCCCCCACCAAGTTCATGTAAACCCCGCCTCTTTCGGATTCTCCCTTGAAGACCACCAGCTCCCAAACACTCAGCCTTAAAATGTGCGCCTGCGGGCACCCCTTTCCCGCTCCACCTCGGCTCCCAATGACTCTTTGCTTCTTCCGTCGCGTGCTAGGGCCCGGAAGCCCTGTTCCCGGCCCGACACCCCCGCCTCACGCTGCCCTCTGCCCGCAG
Seq C2 exon
GTGCTGGCAGAGGAGCGCACCGAGCGCACCGCCCGGGGACTACTGCTGCGCAGGCTGCGGCGCCGGGACTCGGGCGTGTACTTGTGCGCCGCCGTCGAGCAGGGCTTTACGCAACCGCTGCGTCGCCTGTCGCTGCACGTGTTGAGTGCTACGCAGGCCGAACGACTGGCGCGGGCCGAGGAGGCTGCGCCCGCCGCGCCGCCGGGCCCCAAACTCTGGTACCGGGACTTTCTGCAGCTGGTGGAGCCGGGCGGAGGTGGCAGCGCGAACTCCCTGCGCATGTGCCGCCCGCAGCCTGCGCTGCAGTCACTGCCCCTGGAGTCGCGGAGAAAGGGCCGTAACCGGAGGACCCACGCCCCTGAGCCTCGCGCTGAGCGGGGGCCGCGCAGCGCAACGCACTGGTGACCAGACTGTCCCCACGCCGGGAACCAAGCAGGAGACGACAGGCGAGAGAGGAGCCAGACAGACCCTGAAAAGAAGGACGGGTTGGGGCCGGGCACATTGGGGGTCACCGGCCGATGGAGACACCAACCGACAGGCCCTGGCTGAGGGCAGCTGCGCGGGCTTATTTATTAACAGGATAACCCTTGAATGTAGCAGCCCCGGGAGGGCGGCACAGGTCGGGCGCAGGATTCAGCCGGAGGGAAGGGACGGGGAAGCCGAGCTCCAGAGCAACGACCAGGGCCGAGGAGGTGCCTGGAGTGCCCACCCTGGGAGACAGACCCCACCTCCTTGGGTAGTGAGCAGTGAGCAGAAAGCTGTGAACAGGCTGGGCTGCTGGAGGTGGGGCGAGGCAGGCCGACTGTACTAAAGTAACGCAATAAACGCATTATCAGCCAAAGCTGGAATGGCCCCAGCAGAAAACCCCAGTCCTCGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.470
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(14.1=19.1),PF0768612=V-set=FE(45.5=100)
A:
NA
C2:
PF0768612=V-set=PD(45.5=34.1)
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:
CAAGGTGTTCGGCGTGGAG
R:
CTCCACCAGCTGCAGAAAGTC
Band lengths:
358-815
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