MmuINT0141289 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124480714-124480990:+
Coord C1 exon
chr2:124480714-124480776
Coord A exon
chr2:124480777-124480888
Coord C2 exon
chr2:124480889-124480990
Length
112 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TTTTTTTTTTTTTCCTTCAGGAT
3' ss Score
13.28
Exon sequences
Seq C1 exon
AAGCTGACGTGGAGGTCCAGACAGCAGGATCGAGAAAATTGTGCTATGAAAGGCAAGCATAAA
Seq A exon
GTGAGTGCAGTGGACGGGTGCCTGCCACAGTCTCCTCTCGGTGGCTTTGCCACCATGACATCACCATGGGAGATGTCTGACTGCCGTGTGATTTTTTTTTTTTTTCCTTCAG
Seq C2 exon
GATGAATGCCACAACTTCATCAAAGTCTTTGTCCCAAGAAATGATGAGATGGTTTTTGTCTGTGGTACCAATGCTTTCAACCCGATGTGCAGATACTATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199239:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.190 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(4.7=100)
A:
NA
C2:
PF0140314=Sema=FE(7.8=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:
AAGCTGACGTGGAGGTCCA
R:
ATAGTATCTGCACATCGGGTTGA
Band lengths:
162-274
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: