MmuINT0141281 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124484146-124484555:+
Coord C1 exon
chr2:124484146-124484301
Coord A exon
chr2:124484302-124484381
Coord C2 exon
chr2:124484382-124484555
Length
80 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCGCCTCTTTCCCCCACTAGGTA
3' ss Score
11.09
Exon sequences
Seq C1 exon
GCCTGGCTGTTGTGCCAAACACGGCCTCGCAGAAGCTTACAAGACCTCCATCGACTTTCCAGATGACACCCTGGCTTTCATCAAGTCCCACCCGCTGATGGACTCTGCCGTCCCACCCATTGCCGATGAGCCCTGGTTCACAAAGACACGGGTCAG
Seq A exon
GTGAGACCACAGGTCGTCTACTCCTACCCTTCTCTCCTGTCACAGGCCTCCTGATCTGACCCGCCTCTTTCCCCCACTAG
Seq C2 exon
GTACAGGTTGACAGCCATCGAAGTGGACCGTTCAGCAGGGCCATACCAAAACTACACAGTCATCTTTGTTGGCTCTGAAGCTGGCGTGGTACTTAAAGTTTTGGCAAAGACCAGTCCTTTCTCTCTGAATGACAGTGTATTACTCGAAGAGATTGAAGCTTATAACCCAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199239:12
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=FE(12.2=100)
A:
NA
C2:
PF0140314=Sema=FE(13.6=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:
GCCTCGCAGAAGCTTACAAGA
R:
CTGAACGGTCCACTTCGATGG
Band lengths:
168-248
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: