MmuINT0141091 @ 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
chr14:31221121-31221611:+
Coord C1 exon
chr14:31221121-31221240
Coord A exon
chr14:31221241-31221520
Coord C2 exon
chr14:31221521-31221611
Length
280 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CCTTTCCTCTCTCTAACTAGCAT
3' ss Score
9.72
Exon sequences
Seq C1 exon
ACGGAGTGTGCCAACTTCGTGCGGGTCTTACAACCCCATAACCGGACCCATCTGCTGGCCTGTGGCACAGGAGCCTTCCAACCCATCTGCACCTTCATCACAGTGGGGCATCGAGGGGAG
Seq A exon
GTGAGCCTGGGCCTTCCCATGAGAAGCTGAGAAGCTGTGACATTTCCTCCCTGCTGTCTCAAGGCTTCCCATTCAACCAGGGCAGGGCAGAGGGGGCAGGGGCTTGAAAGGCGCCTTTGTGCTGGGGTGCTGAGCCCAACAGAGGTGCTGACCCCATGAAATGAGGATCTTTTCCCCCCCGCCCCCGACCCGATGCTCCAGTTGCACGCAAAGATCACGGTCGAGGCTCTGCTTCTTTCCCAGGTGACCCCGTTCACGCCCCTTTCCTCTCTCTAACTAG
Seq C2 exon
CATGTGCTCCGCTTGGATGCTAGCAGCGTCGAGAATGGAAGGGGGCGTTGCCCACATGAGCCCAGCCGACCCTTCGCCAGCACCTTTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021904:ENSMUST00000090180:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.355
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.7=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:
CGGAGTGTGCCAACTTCGTG
R:
CTACAAAGGTGCTGGCGAAGG
Band lengths:
210-490
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