MmuINT0141008 @ 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
chr9:107506138-107506531:-
Coord C1 exon
chr9:107506374-107506531
Coord A exon
chr9:107506201-107506373
Coord C2 exon
chr9:107506138-107506200
Length
173 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCC
5' ss Score
5.96
3' ss Seq
CCTGTGTTCCCTCCCCATAGCTG
3' ss Score
11.88
Exon sequences
Seq C1 exon
AATTACAGGCCCGGCATGGTGTCCGAACCTTCAGGCTGGAGCGGACCTGCTGTTATGAAGCCTTGCTGGTGGATGAGGAGCGTGGACGCCTGTTTGTGGGTGCTGAGAACCACGTGGCTTCCCTCAGCCTGGACAACATCAGCAAGCGAGCCAAGAAG
Seq A exon
GTGCCCGGGACCCCTAACCTTACTCAGCGTCAGTGCTGGCTCAGGAAAAAGCCTTAGGGTCCCAATCCAGTCTGTCTAGACTCTAGAGAATCTCCAAGGGGTGGGCAACTGAATAGAGAAACCCCCAAAATAAAGAGCGCCCCAAATCCCTAACCTGTGTTCCCTCCCCATAG
Seq C2 exon
CTGGCCTGGCCCGCCCCCGTGGAATGGCGTGAAGAATGCAACTGGGCAGGGAAGGACATTGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(7.7=64.2)
A:
NA
C2:
PF0140314=Sema=FE(4.5=100)
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:
AATTACAGGCCCGGCATGGT
R:
AATGTCCTTCCCTGCCCAGTT
Band lengths:
218-391
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: