HsaINT0147295 @ hg19
Intron Retention
Gene
ENSG00000001617 | SEMA3F
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:HGNC Symbol;Acc:10728]
Coordinates
chr3:50211226-50211547:+
Coord C1 exon
chr3:50211226-50211386
Coord A exon
chr3:50211387-50211484
Coord C2 exon
chr3:50211485-50211547
Length
98 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGG
5' ss Score
4.89
3' ss Seq
TCTGACCCCCCTCTCTGCAGATA
3' ss Score
11.6
Exon sequences
Seq C1 exon
AGCTGAAGGCCACAGGCACCGCCCACTTCTTCAACTTCCTGCTCAACACAACCGACTACCGAATCTTGCTCAAGGACGAGGACCACGACCGCATGTACGTGGGCAGCAAGGACTACGTGCTGTCCCTGGACCTGCACGACATCAACCGCGAGCCCCTCATT
Seq A exon
GTAAGGGCTGGCCCTGATGTGGGACGTGGGGTGGGCACGGAGCCCCAGGGCTCAGGGCATGTCCAGAAGGCTGCACCTTCTGACCCCCCTCTCTGCAG
Seq C2 exon
ATACACTGGGCAGCCTCCCCACAGCGCATCGAGGAATGCGTGCTCTCAGGCAAGGATGTCAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000001617-SEMA3F:NM_004186:3
Average complexity
IR-S
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:
PF135771=SnoaL_4=PD(53.9=74.5),PF0140314=Sema=WD(100=65.5)
A:
NA
C2:
PF0140314=Sema=FE(15.0=100)
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:
TGCTCAACACAACCGACTACC
R:
GACATCCTTGCCTGAGAGCAC
Band lengths:
182-280
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)