MmuINT0141005 @ mm9
Intron Retention
Gene
ENSMUSG00000057969 | Sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:MGI Symbol;Acc:MGI:107561]
Coordinates
chr9:107501908-107502189:-
Coord C1 exon
chr9:107502134-107502189
Coord A exon
chr9:107502048-107502133
Coord C2 exon
chr9:107501908-107502047
Length
86 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTTACATCTTTTGTCTCAAGACT
3' ss Score
5
Exon sequences
Seq C1 exon
ACGGTTCCGGAGGCAAGACATAAGGAATGGCGACCCCAGCACCCTATGCTCTGGAG
Seq A exon
GTGAGTACCCCAATCAGCTTCTGTCCTCGGCCCTTGAAATTGCCACACCCAAGCCTTGTCTGAACTTTTACATCTTTTGTCTCAAG
Seq C2 exon
ACTCTTCTCACTCTGTGCTGCTGGAGAAGAAGGTGTTGGGTGTGGAGAGCGGCAGCGCGTTTCTGGAGTGTGAGCCCCGCTCGCTCCAGGCGCATGTGCAGTGGACCTTCCAAGGTGCAGGGGAGGCAGCTCACACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(29.7=100),PF0768612=V-set=PU(0.1=0.0)
A:
NA
C2:
PF0143720=PSI=PD(14.1=19.1),PF0768612=V-set=PU(48.9=97.9)
Main Inclusion Isoform:
NA
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:
GACATAAGGAATGGCGACCCC
R:
TGTGAGCTGCCTCCCCTG
Band lengths:
175-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: