MmuINT0141084 @ mm10
Intron Retention
Gene
ENSMUSG00000021904 | Sema3g
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G [Source:MGI Symbol;Acc:MGI:3041242]
Coordinates
chr14:31223289-31223701:+
Coord C1 exon
chr14:31223289-31223520
Coord A exon
chr14:31223521-31223609
Coord C2 exon
chr14:31223610-31223701
Length
89 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CCTTTTTTCCCCTGCTCCAGATT
3' ss Score
9.51
Exon sequences
Seq C1 exon
TGTCCTAGCAAGATGACCGCACAGCCAGGCCGACCCTTTGGCAGCACCAAGGACTACCCAGACGAGGTGTTGCAGTTTGTCCGAGACCACCCACTCATGTTCCAGCCTGTGAGGCCTCGGCGTGGCCGCCCTGTCCTGGTCAAAACTCACTTGGCTCAGCGACTGCGCCAGATTGTGGTGGATCGAGTGGAGGCTGAGGATGGGACCTATGATGTCATCTTCCTAGGGACTG
Seq A exon
GTAAGAGGGCTGACCAGAGGCAGCCAGCTATGTGGGGAGAATGTAGCTTCTTCCTGCTTGTCTCACTAACCTTTTTTCCCCTGCTCCAG
Seq C2 exon
ATTCGGGTTCTGTGCTCAAAGTCATTGCCCTCCAGGGTGGTGGCTTGACTGAACCTGAAGAGGTGGTTTTGGAGGAGCTCCAGGTGTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021904:ENSMUST00000090180:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.128 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.3=100)
A:
NA
C2:
PF0140314=Sema=FE(6.7=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:
AGACCACCCACTCATGTTCCA
R:
GGAGGGCAATGACTTTGAGCA
Band lengths:
182-271
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