MmuINT0140999 @ 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
chr9:107503689-107503984:-
Coord C1 exon
chr9:107503915-107503984
Coord A exon
chr9:107503834-107503914
Coord C2 exon
chr9:107503689-107503833
Length
81 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GCTCTCTCCATTGCCTGCAGTGG
3' ss Score
6.65
Exon sequences
Seq C1 exon
AGGATGTTTTCCTTCTGTCCTCCCGAGACCGCCAGACACCTCTTCTCTATGCTGTCTTCTCCACCTCCAG
Seq A exon
GTGAGGGGCAGGAAGCAGTTCCCTTGGGCAGCCAGTTGAGTTTGCCGGGGTTCCTCACTCTGCTCTCTCCATTGCCTGCAG
Seq C2 exon
TGGTGTCTTCCAGGGCTCTGCTGTGTGCGTGTACAGCATGAACGATGTGCGCCGAGCCTTCTTGGGACCTTTTGCTCACAAAGAGGGGCCTACACACCAGTGGGTGTCCTACCAGGGTCGTGTCCCCTACCCAAGACCTGGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:10
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(5.2=100)
A:
NA
C2:
PF0140314=Sema=FE(10.8=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:
CCGCCAGACACCTCTTCTCTA
R:
CAGGTCTTGGGTAGGGGACAC
Band lengths:
182-263
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: