MmuINT0141012 @ 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
chr9:107504291-107505324:-
Coord C1 exon
chr9:107505205-107505324
Coord A exon
chr9:107504437-107505204
Coord C2 exon
chr9:107504291-107504436
Length
768 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
CGTGCCTCCTGTTTTGCTAGAAC
3' ss Score
7.48
Exon sequences
Seq C1 exon
GGGAAGAACTGTATTCTGGGGTGACAGCAGACCTTATGGGCCGGGACTTTACCATCTTTCGAAGCCTTGGTCAGAATCCGAGTCTCCGAACAGAGCCCCATGATTCCCGCTGGCTCAATG
Seq A exon
GTGAGACACTGGTGGGGACCCTGGGAGGGGGCTGCCCTCCTCCGATAGGGAAGGTGCCACAGAATGAGGGAGCCACATTGAAGTCTCTCCATGTATCTACTATAATCCCTGAGCCAGAGGCACAGAGGCAGAGGCAGGCAGGAGTCTTTGAGCCCATGGGTCTTGGAGCCAGGATATGCTGAGGTACATGCCAGTGGCCGTGCAAGATGAAAGAACAGAAAAGGAAAAAGGTGTCTGGGTTGAATAAGGGAAGCTATTGTTGGGAGGGGCTGTGGGTTATTAATAGCTTCCAGAACACAAGAAAGCCAGCCAACAGAACTGGATGAGCATTCTAGGTAAGGGAAATGATGAGCGCAAAGGCCCTGAGGCAAAAAACCAGCAAAGATAAGGCTCAAGCAACTAGCATTGATAGGAAACTCAGACTCTCAAGGGCTGGAGTCCTTTAGCATGGGACAGCATGAGAAACCGAAACAGGAACAGGGAGTATTTGATCTGCTAGGGAGGAAGATTTGTGAATGAAGGTGAAAACAGATACCCGATCTCCCTCTTTTCCTGGCAAATTAAGGAAGTGTGGCATGGTCAGAAAGCCCTGTAAAGGGGAGAGGAGCAGCCCGCTTGCGCTCGTAGCTATGGTCTCTACTGCCCCCTCGTGGCTGCTTCTTGCCTTGCAGATGCCGATCATAGGGTGGGTCTTGGAGGCTCTGGTTGTGAGATCCTTGTCATGGACCAGGACCAGGCCCGCTGATACCGTGCCTCCTGTTTTGCTAG
Seq C2 exon
AACCCAAGTTTGTCAAGGTCTTTTGGATCCCAGAGAGTGAGAACCCTGATGACGATAAAATCTATTTCTTCTTCCGCGAGTCCGCTGTGGAAGCAGCACCAGCAATGGGGCGCATGTCTGTGTCTCGTGTTGGCCAGATCTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.098 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.0=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:
AGAACTGTATTCTGGGGTGACA
R:
CCTGCAGATCTGGCCAACAC
Band lengths:
262-1030
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: