MmuALTD0012568-2/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000034684 | Sema3f
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:MGI Symbol;Acc:MGI:1096347]
Coordinates
chr9:107684688-107685547:-
Coord C1 exon
chr9:107685371-107685547
Coord A exon
chr9:107685344-107685370
Coord C2 exon
chr9:107684688-107684776
Length
27 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCTT
5' ss Score
3.62
3' ss Seq
TCCTGCCCGGCCCGTTCCAGACC
3' ss Score
6.64
Exon sequences
Seq C1 exon
TGCCCTGGTGGAACCTTCACGCCCTCGATGAAGTCCACTAAGGACTACCCTGATGAAGTGATCAACTTCATGCGCACTCATCCGCTCATGTACCAGGCCGTCTACCCGCTCCAGCGGCGACCCCTGGTGGTCCGTACAGGCGCTCCCTACCGCCTCACCACTGTCGCTGTGGACCAG
Seq A exon
GTGGATGCAGCTGATGGACGCTATGAG
Seq C2 exon
ACCGCGGGACAGTGCAGAAGGTCATCGTGCTGCCCAAGGACGACCAGGAGGTGGAAGAGCTGATGCTAGAGGAAGTGGAGGTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034684-37-35,38-35,39-35-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.180 A=NA C2=0.087
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(61.3=100)
A:
NA
C2:
PF0140314=Sema=FE(6.6=100)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATGTACCAGGCCGTCTACC
R:
CGATGACCTTCTGCACTGTCC
Band lengths:
119-146
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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