MmuINT0141079 @ 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
chr9:107687949-107688349:-
Coord C1 exon
chr9:107688230-107688349
Coord A exon
chr9:107688089-107688229
Coord C2 exon
chr9:107687949-107688088
Length
141 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
CCACCTCCCCCCCCTTCCAGATC
3' ss Score
12.58
Exon sequences
Seq C1 exon
ATGAGGAACTCTATGCAGGAGTGTACATCGATTTTATGGGTACCGATGCAGCCATTTTCCGCACGCTGGGGAAGCAGACAGCCATGCGCACAGATCAGTACAACTCCCGGTGGCTCAATG
Seq A exon
GTGAGCTCCACCTGCAAAGACCTGAGTGGGAAGTGTGGCCGGATGTGCCAAGACCTGCACGCCTCGGGGAGAGTTTAAACCTGTGACTAACTTGGGGCAGGTTCATGCTGCCATCTCCTAACCACCTCCCCCCCCTTCCAG
Seq C2 exon
ATCCTTCCTTCATACATGCTGAGCTCATCCCTGACAGTGCAGAGCGCAATGACGATAAACTCTACTTCTTCTTCCGAGAGCGCTCGGCAGAGGCGCCACAGAACCCTGCTGTGTATGCCCGCATCGGGCGCATCTGCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034684:ENSMUST00000080560:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.072 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.0=100)
A:
NA
C2:
PF0140314=Sema=FE(10.4=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:
AGGAACTCTATGCAGGAGTGT
R:
GATGCGGGCATACACAGCAG
Band lengths:
242-383
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