MmuINT0141072 @ 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
chr9:107683560-107684040:-
Coord C1 exon
chr9:107683973-107684040
Coord A exon
chr9:107683694-107683972
Coord C2 exon
chr9:107683560-107683693
Length
279 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
AGGGTCCTCTTGATCCACAGCAA
3' ss Score
5.9
Exon sequences
Seq C1 exon
GCGGAGTCGCCGGCAAGATGTCCGCCACGGGAACCCTATCAGACAGTGCCGTGGTTTCAATTCCAATG
Seq A exon
GTAAGTAAGCCCATGGCACCTCCTGTAGCGGCTTCTCGTGTTTTAGAGTCCAATGCGCCCAAAGCCCGCAGACACCCTCAGAGTCCAGACTTGCGTATGGTGCCCTGGGTGGCAGGATGGGTGGCCTTAGGTCTGGGATTAGGAAGCCACCTCAATGGAGAGTCACCCAGCGATGTGGTCCTGTTTGGTGTGTGGGTGCCCCTTGCTGTCTGCCTCTCCCTACTGAGCAGACGGCCTGGGAGCAGCGCTGCTTCCACTCAGGGTCCTCTTGATCCACAG
Seq C2 exon
CAAACAAGAATGCCGTAGAGTCTGTGCAGTACGGAGTGGCCGGCAGCGCAGCTTTCCTTGAGTGTCAGCCCCGCTCACCTCAAGCCACTGTCAAGTGGCTGTTCCAGCGAGATCCCAGTGATCGGCGCCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034684:ENSMUST00000080560:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.292 A=NA C2=0.089
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(32.1=70.8)
A:
NA
C2:
PF0767911=I-set=PU(45.5=88.9)
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:
GGAGTCGCCGGCAAGATG
R:
ATCACTGGGATCTCGCTGGAA
Band lengths:
188-467
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