MmuINT0141010 @ 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
chr9:107603122-107603416:-
Coord C1 exon
chr9:107603297-107603416
Coord A exon
chr9:107603216-107603296
Coord C2 exon
chr9:107603122-107603215
Length
81 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
CTCCCCTGCCCTGCCCCCAGGAA
3' ss Score
11.56
Exon sequences
Seq C1 exon
ACCGAGTGCATGAACTTCGTGAAGCTGCTGCACACCTACAACCACACCCACTTGCTGGCCTGTGGCACAGGGGCTTTCCACCCAACCTGTGCCTTTGTGGAGGTGGGCCACCGGCTGGAG
Seq A exon
GTAAGACCAGGACTAAACAGTGGAGAGATGGGAAGGGTGACAAAGGACCTGACATTAACAACTCCCCTGCCCTGCCCCCAG
Seq C2 exon
GAACCCATGCTTCAACTGGACCGGAGGAAACTTGAGGACGGCAAGGGGAAGACTCCTTATGACCCAAGGCATCGGGCTGCCTCGGTGCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969:ENSMUST00000102532:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.411
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(33.1=100)
A:
NA
C2:
PF0140314=Sema=FE(7.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGCTGCTGCACACCTACAA
R:
CCGATGCCTTGGGTCATAAGG
Band lengths:
175-256
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