MmuINT0141083 @ mm9
Intron Retention
Gene
ENSMUSG00000021904 | Sema3g
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G [Source:MGI Symbol;Acc:MGI:3041242]
Coordinates
chr14:32036106-32036706:+
Coord C1 exon
chr14:32036106-32036250
Coord A exon
chr14:32036251-32036474
Coord C2 exon
chr14:32036475-32036706
Length
224 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
GTTCCCTCTGCTGCTCCCAGTGT
3' ss Score
6.83
Exon sequences
Seq C1 exon
TGCTGTGTTCCAGGGCTTTGCTGTCTGTGTGTACCACATGGTAGACATCTGGGAGGTCTTCAATGGGCCCTTTGCCCACCGAGATGGCCCTCAGCATCAGTGGGGACCCTATGGGGGCAAGGTGCCCTTCCCTCGCCCCGGTGTG
Seq A exon
GTAAGTAGCTGCTTGGGGTCAGGCAATAGAGGCCAAAGCAGATGACAGGGAACTCCTGTATAGAAAAGCTTCCGGTTTAACACTCAGCCCACTTGGCAGTAGTGGGCTGAGCCTCCAGAGGGTTTGGGAGGAGAGTCTCTGCTGTGTGCATGACCCCCTGGAGATAGAAAGAGGTTGGGTAGTGCCATCCTAGGGACTTCAAGTGTTCCCTCTGCTGCTCCCAG
Seq C2 exon
TGTCCTAGCAAGATGACCGCACAGCCAGGCCGACCCTTTGGCAGCACCAAGGACTACCCAGACGAGGTGTTGCAGTTTGTCCGAGACCACCCACTCATGTTCCAGCCTGTGAGGCCTCGGCGTGGCCGCCCTGTCCTGGTCAAAACTCACTTGGCTCAGCGACTGCGCCAGATTGTGGTGGATCGAGTGGAGGCTGAGGATGGGACCTATGATGTCATCTTCCTAGGGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021904-Sema3g:NM_001025379:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.128
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.8=100)
A:
NA
C2:
PF0140314=Sema=FE(17.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCTTTGCTGTCTGTGTGTA
R:
GTCGCTGAGCCAAGTGAGTTT
Band lengths:
296-520
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: