MmuINT0140998 @ mm10
Intron Retention
Gene
ENSMUSG00000057969 | Sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:MGI Symbol;Acc:MGI:107561]
Coordinates
chr9:107604969-107605587:-
Coord C1 exon
chr9:107605447-107605587
Coord A exon
chr9:107605156-107605446
Coord C2 exon
chr9:107604969-107605155
Length
291 bp
Sequences
Splice sites
5' ss Seq
GAAGTGGGT
5' ss Score
2.85
3' ss Seq
TGCGGACTCTTCTCTTCCAGATC
3' ss Score
9.95
Exon sequences
Seq C1 exon
CAACTGCTTTGCTCTTTGCACTTGGTGCCCTCTGGAATGACCACAGGATCTGACTCTCATCTGTCGGCTCTTCGCCCTTTACTGCCTGGGGACCTTGTCCGCATCATCAGTATCCTTGTCTCTGCCCCAGGCTGGCATGAA
Seq A exon
GTGGGTGCACAGTGTTTGTGAATTAACGTCTGTGAGTGTGTGTGCGGAGGGGAGGTTACTGAGGGTGACGTGGTGGGGCGGGTGCCTGCCAATGCAGGGTGACCCTGAGGGTGTGCCCGGTGTGGGTGTGTCTCTGATTGTGGCCAGGCGGGGCACCCTTGGTGGAGAGGAAACGGTATGCGACCCCCCAGCCTCTATCCCTAGGGGCTGTAATCTGATCCCTTGGGACTCCCCCGTGCCCTCCCACCCGCCCTTACCCTCTCTGCTTTGCTGCGGACTCTTCTCTTCCAG
Seq C2 exon
ATCCTGGGGCAGAGTCCAGGACTGCTGAAGGCTCCTCCACACACGCCTGCTGAACCCTGAGCGCCCTGAGCTGCCGGCATGGGGCGGGCTGAGGCCGCCGCCATGATCCCAGGCCTGGCCCTTCTCTGGGTAGCAGGGCTAGGGGATACTGCCCCTAACCTTCCCCGCCTTCGGCTCTCCTTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969:ENSMUST00000102532:3
Average complexity
IR
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 Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGGTGCCCTCTGGAATGAC
R:
GAAGGCGGGGAAGGTTAGGG
Band lengths:
293-584
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types