HsaINT0147286 @ hg38
Intron Retention
Gene
ENSG00000001617 | SEMA3F
Description
semaphorin 3F [Source:HGNC Symbol;Acc:HGNC:10728]
Coordinates
chr3:50183186-50183564:+
Coord C1 exon
chr3:50183186-50183255
Coord A exon
chr3:50183256-50183419
Coord C2 exon
chr3:50183420-50183564
Length
164 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
AGCGCCTGCCATGCCCACAGCTC
3' ss Score
7.03
Exon sequences
Seq C1 exon
AGGACGTGTTTGTCCAGCAGACCCAGGACGTGAGGAACCCTGTCATTTACGCTGTCTTTACCTCCTCTGG
Seq A exon
GTGAGGCTGGGGTCAGGGCCAGCAGTGGCAGGGAGTGGCCCCGTTGGGGGATTGTAACTCGTGGAGAACCCCAGCCCGGTGGCGAGCTGTGGGGAGGGGGCAGTTTGGGGAGGGGCCCTAGGTGGAGGGTCTGTCCTGCTCAGCAGCGCCTGCCATGCCCACAG
Seq C2 exon
CTCCGTGTTCCGAGGCTCTGCCGTGTGTGTCTACTCCATGGCTGATATTCGCATGGTCTTCAACGGGCCCTTTGCCCACAAAGAGGGGCCCAACTACCAGTGGATGCCCTTCTCAGGGAAGATGCCCTACCCACGGCCGGGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000001617:ENST00000002829:11
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=0.037
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(4.9=100)
A:
NA
C2:
PF0140314=Sema=PD(14.6=95.9)
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:
GACGTGTTTGTCCAGCAGACC
R:
CCGTGGGTAGGGCATCTTCC
Band lengths:
204-368
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