MmuINT0141094 @ 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
chr14:32035180-32035636:+
Coord C1 exon
chr14:32035180-32035325
Coord A exon
chr14:32035326-32035521
Coord C2 exon
chr14:32035522-32035636
Length
196 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGA
5' ss Score
5.46
3' ss Seq
ATTCCCCCTCCCTTCCCCAGAAT
3' ss Score
10.7
Exon sequences
Seq C1 exon
AACCCCGGTTTGTGATGGCTGCTCGGATCCCAGATAACTCTGACCGGGACGACGACAAGGTGTACTTCTTCTTCTCCGAGACTGTCCCGTCACCAGATGGTGGCCCAGGTCATGTCACCATCAGCCGAGTGGGCCGCGTCTGTGTG
Seq A exon
GTGAGAGCCGTGGTGGGGTGGGGAGGTTCGAGTCCCCTGTTGTGACCTCTTTCCTGGACTGTCCCTTCACAGTAGAGAAACTGAGGCTAGGATACAGTGCTAACATACATCCGTCTCTCTGTGGTTGAGAGTAGAAGAACAGGAGGCGGGTCCCATACTCAGGGGGCATAAAGCTGATTCCCCCTCCCTTCCCCAG
Seq C2 exon
AATGATGCTGGTGGCCAGCGGGTGCTGGTGAACAAATGGAGCACTTTCCTCAAGGCCCGGCTGGTGTGCTCTGTGCCTGGCCCGGGTGGGGCTGAGACTCACTTTGACCAGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021904-Sema3g:NM_001025379:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.8=100)
A:
NA
C2:
PF0140314=Sema=FE(8.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGTGATGGCTGCTCGGATC
R:
TCAAAGTGAGTCTCAGCCCCA
Band lengths:
245-441
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: