MmuINT0141269 @ mm9
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94970928-94971398:+
Coord C1 exon
chr3:94970928-94971042
Coord A exon
chr3:94971043-94971334
Coord C2 exon
chr3:94971335-94971398
Length
292 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAA
5' ss Score
6
3' ss Seq
CCTCCTTACCTACCCTTCAGGGA
3' ss Score
9.93
Exon sequences
Seq C1 exon
GTGCCTCTCCATCATCCTGGTTCCGGGGCCTGGAGGACGATGCTGTGGCTGCGGAACTTGGGCTGGACTTTCAGAGATTCCTGACCTTGAACCGGACCTTGCTTGTGGCTGCCCG
Seq A exon
GTAAAATGGCCGAGGCACCGTTGTGGGGCAGACATGCATGATCCTGGGCAGACATGGGACCTGCATGGCCACTGCAGCATCTTGCAGGGGACACATGCAGGTGCACAAGCCATGGGACATGGACATGCTTGGACCCAGAGAACATATGCCAAGGCATGGAGTGAGGGGGAGGCTAGGGATCAGGAACTTTGTGTGGCTTGGCCCTGAGCTGGTGAATATGGGTAAGGAGGGGCTAAGCAGCTCAGGCAGGGTGCCTCTGCTCAGCCCTGACCCCTCCTTACCTACCCTTCAG
Seq C2 exon
GGATCACGTTTTCTCCTTCGATCTTCAAGCCCAAGAAGAAGGGGAGGGGCTGGTGCCCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-Sema6c:NM_011351:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(11.0=35.9)
A:
NA
C2:
PF0140314=Sema=FE(16.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCCTCTCCATCATCCTGGTT
R:
AGCCCCTCCCCTTCTTCTTG
Band lengths:
165-457
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: