MmuINT0141265 @ mm9
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94974673-94975172:+
Coord C1 exon
chr3:94974673-94974819
Coord A exon
chr3:94974820-94975094
Coord C2 exon
chr3:94975095-94975172
Length
275 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CACAGCTCAGTTTCCCCTAGGAG
3' ss Score
2.63
Exon sequences
Seq C1 exon
GTGCAGTGGGAAGCGGTCACCCCGAGCTGCGCGGCGGATCATAGGGCTGGAGCTGGACACTGAGGGTCACAGGCTTTTTGTGGCCTTTCCTGGATGTATCGTCTACCTCTCTCTCAGCCGGTGTGCCCGGCATGGAGCATGTCAGAG
Seq A exon
GTGAGAGGAGCCTAAGTTCCATGCTGCCTGGCTACACTTTCGGGGTTAGTAGGAGCTCAGAAAAATCCCCAAGTCTTGAGGGTAGCAAGGAAATGGAGGAGAGGGTGGGCACCTTGGGTAGTCTGAAGTAGGCAGCCACGAGGGTCTGGAGCAGATTGAAGTGGATGGGATGGAAATACTGGGGGACGGGGGAGGCTCTCTCTCATAAGCTAGGGTAAATAGAGGGTAACGGTGAGTGGAGGGGTAGCAGCCTCACACAGCTCAGTTTCCCCTAG
Seq C2 exon
GAGCTGCCTGGCTTCTCTGGACCCATACTGTGGATGGCATCGATCCAGAGGCTGCATGAGTATCAGGGGACCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-Sema6c:NM_011351:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.060 A=NA C2=0.084
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(0.5=4.0),PF0143720=PSI=PU(14.3=18.0)
A:
NA
C2:
PF0143720=PSI=FE(41.3=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:
GTGCAGTGGGAAGCGGTC
R:
AGGTCCCCTGATACTCATGCA
Band lengths:
220-495
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: