HsaINT0147478 @ hg38
Intron Retention
Gene
ENSG00000167680 | SEMA6B
Description
semaphorin 6B [Source:HGNC Symbol;Acc:HGNC:10739]
Coordinates
chr19:4555474-4556089:-
Coord C1 exon
chr19:4555988-4556089
Coord A exon
chr19:4555565-4555987
Coord C2 exon
chr19:4555474-4555564
Length
423 bp
Sequences
Splice sites
5' ss Seq
AGCGTGAGT
5' ss Score
8.2
3' ss Seq
AGGCCCCATGGTCCCTGCAGATA
3' ss Score
6.83
Exon sequences
Seq C1 exon
GGCGAGTGTCGAAACTTCGTAAAGGTGCTGCTCCTTCGGGACGAGTCCACGCTCTTTGTGTGCGGTTCCAACGCCTTCAACCCGGTGTGCGCCAACTACAGC
Seq A exon
GTGAGTCTTCAGACTCCCTGCGCCCCAGGTCCAACCTCCAGGCCTCTGCTCGCCCGACCTCCGCTGGCCATGGCTTTTCCCCAGGCCGTGTCACCTCCTCCAGGAAGCCTTCCTGGATATACTCTCCCTGCCTCCTCCCCCTGAGCTCAAGAGGAGTCAGCGCTGTCCAAACGAGGCCTGTACAGGGGGCCGGGGAAGCCGTAGCTACTTAGGTAATGAGCCAGTTACAGGTCTAACTAGGCATTGACTCTTAAACCCATTTACAGATCAGTAAACTGAGGCCCTGAGAGGTTAAGTGAGTGGCCAAGGTCACACAGTAATCCGTGGTGGATCAGGATTCCCCCTGGAGTGGGGGGCTGAGGGAGCCAGGGGCTGCTAGGTGGGGTCAGGAGATCTGTCACTCAGGCCCCATGGTCCCTGCAG
Seq C2 exon
ATAGACACCCTGCAGCCCGTCGGAGACAACATCAGCGGTATGGCCCGCTGCCCGTACGACCCCAAGCACGCCAATGTTGCCCTCTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167680:ENST00000586582:6
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(16.7=100)
A:
NA
C2:
PF0140314=Sema=FE(15.2=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:
CGAAACTTCGTAAAGGTGCTGC
R:
CAGAGAAGAGGGCAACATTGG
Band lengths:
184-607
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