MmuINT0141013 @ 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
chr9:107504091-107504436:-
Coord C1 exon
chr9:107504291-107504436
Coord A exon
chr9:107504203-107504290
Coord C2 exon
chr9:107504091-107504202
Length
88 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CCTTCTGATCCTGTGAGCAGAAT
3' ss Score
5.62
Exon sequences
Seq C1 exon
AACCCAAGTTTGTCAAGGTCTTTTGGATCCCAGAGAGTGAGAACCCTGATGACGATAAAATCTATTTCTTCTTCCGCGAGTCCGCTGTGGAAGCAGCACCAGCAATGGGGCGCATGTCTGTGTCTCGTGTTGGCCAGATCTGCAGG
Seq A exon
GTAAGGAGACACTAGGCCAATTCTACCTTTGCCCCTGACCCTTTGCCTGCGATGGTCTTGCTCTCATCCCTTCTGATCCTGTGAGCAG
Seq C2 exon
AATGACCTGGGTGGCCAGCGGAGCTTGGTCAACAAATGGACCACATTTCTGAAGGCGCGGCTTGTGTGCTCAGTACCTGGAGTTGAGGGTGACACCCACTTTGACCAACTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:8
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=FE(10.8=100)
A:
NA
C2:
PF0140314=Sema=FE(8.4=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:
CCCAGAGAGTGAGAACCCTGA
R:
CGCCTTCAGAAATGTGGTCCA
Band lengths:
175-263
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: