HsaINT0147296 @ hg38
Intron Retention
Gene
ENSG00000001617 | SEMA3F
Description
semaphorin 3F [Source:HGNC Symbol;Acc:HGNC:10728]
Coordinates
chr3:50174052-50174350:+
Coord C1 exon
chr3:50174052-50174114
Coord A exon
chr3:50174115-50174230
Coord C2 exon
chr3:50174231-50174350
Length
116 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGT
5' ss Score
9.54
3' ss Seq
AGCCTTCCCTGTGGCCCCAGGGC
3' ss Score
7.5
Exon sequences
Seq C1 exon
ATACACTGGGCAGCCTCCCCACAGCGCATCGAGGAATGCGTGCTCTCAGGCAAGGATGTCAAC
Seq A exon
GTGAGTTTGGTGGGATCCACAGGTGGGAAGGGGGAATCCACAGGTGGGAAGGTACTGCCCCCAGTGAGGGGGCAGGCCTGGCCAGGGCACCTATGCAGCCTTCCCTGTGGCCCCAG
Seq C2 exon
GGCGAGTGTGGGAACTTCGTCAGGCTCATCCAGCCCTGGAACCGAACACACCTGTATGTGTGCGGGACAGGTGCCTACAACCCCATGTGCACCTATGTGAACCGCGGACGCCGCGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000001617:ENST00000002829:4
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(15.0=100)
A:
NA
C2:
PF0140314=Sema=FE(18.8=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:
ATACACTGGGCAGCCTCCC
R:
GTCCGCGGTTCACATAGGTG
Band lengths:
172-288
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