MmuINT0141003 @ 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
chr9:107502281-107502702:-
Coord C1 exon
chr9:107502661-107502702
Coord A exon
chr9:107502439-107502660
Coord C2 exon
chr9:107502281-107502438
Length
222 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GAGACTCTTGTGCCCTCTAGCAA
3' ss Score
4.56
Exon sequences
Seq C1 exon
GACTCTGCCGCTATCACCAGCATGCAAATCTCCTCTAAAAGG
Seq A exon
GTGAGTAACTCAACTTGGGGAAGAAGTGACCCTGTCCCACAGCCCCCCAGCTGTCTAGCTTCTCCTTGGTTTTCAAAGCCCCGAGTTTCAGGTCTAGCTTCTCTTTGCTAGACAATGCGAACCTCAGTGTTCCCACCTGTCCAGAGGGGGAAAGGCTATCTGACTGAAGGGAACCAGGTAAGGGCTGTCCTCCATCAGACTGGAGACTCTTGTGCCCTCTAG
Seq C2 exon
CAACAACTCTACATAGCATCGCGCAGCGCAGTGGCCCAGATTGCTTTGCATCGCTGCACTGCCCTAGGCCGCGCCTGCGCAGAATGCTGCTTGGCCCGTGATCCTTACTGCGCCTGGGATGGATCAGCTTGCACACGCTTCCAGCCTACGGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:14
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(2.9=100)
A:
NA
C2:
PF0143720=PSI=PU(54.7=66.0)
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:
CTGCCGCTATCACCAGCATG
R:
CGTAGGCTGGAAGCGTGTG
Band lengths:
188-410
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: