MmuINT0141080 @ mm10
Intron Retention
Gene
ENSMUSG00000034684 | Sema3f
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:MGI Symbol;Acc:MGI:1096347]
Coordinates
chr9:107687730-107688088:-
Coord C1 exon
chr9:107687949-107688088
Coord A exon
chr9:107687845-107687948
Coord C2 exon
chr9:107687730-107687844
Length
104 bp
Sequences
Splice sites
5' ss Seq
CTCGTAAGT
5' ss Score
9.63
3' ss Seq
CTTTCTGCCCCCACCCCCAGAAC
3' ss Score
10.88
Exon sequences
Seq C1 exon
ATCCTTCCTTCATACATGCTGAGCTCATCCCTGACAGTGCAGAGCGCAATGACGATAAACTCTACTTCTTCTTCCGAGAGCGCTCGGCAGAGGCGCCACAGAACCCTGCTGTGTATGCCCGCATCGGGCGCATCTGCCTC
Seq A exon
GTAAGTGTCTAAAAGGCTCTGCTGCCACACCCCAGACCTACCCCAGCTGGTCTTGGGGGCGGTGAATGAACTGATCTAATCTGGCTTTCTGCCCCCACCCCCAG
Seq C2 exon
AACGATGACGGTGGCCATTGCTGCCTGGTCAACAAGTGGAGCACATTCCTGAAGGCTCGGCTCGTCTGCTCCGTGCCAGGCGAGGATGGTATTGAGACCCACTTCGACGAACTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034684:ENSMUST00000080560:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.4=100)
A:
NA
C2:
PF0140314=Sema=FE(8.6=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:
ACATGCTGAGCTCATCCCTGA
R:
GGAGTTCGTCGAAGTGGGTCT
Band lengths:
242-346
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types