MmuINT0140998 @ 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
chr9:107507300-107507733:-
Coord C1 exon
chr9:107507603-107507733
Coord A exon
chr9:107507487-107507602
Coord C2 exon
chr9:107507300-107507486
Length
116 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGC
5' ss Score
8.56
3' ss Seq
TGCGGACTCTTCTCTTCCAGATC
3' ss Score
9.95
Exon sequences
Seq C1 exon
CGGAGGGGAGGTTACTGAGGGTGACGTGGTGGGGCGGGTGCCTGCCAATGCAGGGTGACCCTGAGGGTGTGCCCGGTGTGGGTGTGTCTCTGATTGTGGCCAGGCGGGGCACCCTTGGTGGAGAGGAAACG
Seq A exon
GTATGCGACCCCCCAGCCTCTATCCCTAGGGGCTGTAATCTGATCCCTTGGGACTCCCCCGTGCCCTCCCACCCGCCCTTACCCTCTCTGCTTTGCTGCGGACTCTTCTCTTCCAG
Seq C2 exon
ATCCTGGGGCAGAGTCCAGGACTGCTGAAGGCTCCTCCACACACGCCTGCTGAACCCTGAGCGCCCTGAGCTGCCGGCATGGGGCGGGCTGAGGCCGCCGCCATGATCCCAGGCCTGGCCCTTCTCTGGGTAGCAGGGCTAGGGGATACTGCCCCTAACCTTCCCCGCCTTCGGCTCTCCTTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTGAGGGTGACGTGGTGG
R:
GCCCTGCTACCCAGAGAAGG
Band lengths:
258-374
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: