MmuINT0141272 @ mm9
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94971921-94972311:+
Coord C1 exon
chr3:94971921-94972022
Coord A exon
chr3:94972023-94972220
Coord C2 exon
chr3:94972221-94972311
Length
198 bp
Sequences
Splice sites
5' ss Seq
GGGGTACAG
5' ss Score
0.84
3' ss Seq
AATCTGCTTCCTGTTCCCAGATA
3' ss Score
8.95
Exon sequences
Seq C1 exon
GACGAATGCTACAACTACATCCGTGTTCTTGTTCCCTGGAACTCGCAGACACTTCTTGCCTGTGGAACAAATTCCTTCAGCCCTATGTGCCGCAGCTATGGG
Seq A exon
GTACAGAGGGAAGAGGACTGGGAGGAGAATCTAAAATAAGCTTTCAGTTTGATGGGAAGAGATGGGCATCTGGGAATGGGAGTGGGCATTCGTGGGGTGCAAGAGTGCAGAGGAGCTGGAGAAGGAGATGGGTGGGTGTGCACTGTACGGCCAGACTCTAAGACCCCAAGGTTACAGGAATCTGCTTCCTGTTCCCAG
Seq C2 exon
ATAACATCTCTGCAACAGGAGGGTGAGGAGCTGAGTGGGCAGGCTCGATGCCCCTTTGATGCCACCCAGTCCACTGTGGCCATCTTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-Sema6c:NM_011351:5
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=0.028
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(1.5=83.3)
A:
NA
C2:
PF0140314=Sema=FE(23.6=100),PF0140314=Sema=PU(1.1=9.7)
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:
ACGAATGCTACAACTACATCCGT
R:
CTGCAAAGATGGCCACAGTGG
Band lengths:
192-390
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: