MmuINT0141279 @ mm10
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124657644-124658102:+
Coord C1 exon
chr2:124657644-124657861
Coord A exon
chr2:124657862-124657970
Coord C2 exon
chr2:124657971-124658102
Length
109 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
ATGATTGTATCACTTTTCAGCAT
3' ss Score
7.48
Exon sequences
Seq C1 exon
GCTGTGTATTCCCGCGTGGCTCGCATTTGTAAAAACGACATGGGTGGCTCACAGCGGGTCCTGGAGAAACACTGGACTTCCTTCCTTAAGGCTCGGCTGAACTGCTCCGTTCCTGGAGATTCCTTTTTCTACTTCGACGTCCTGCAGTCTATAACAGACATAATCCAAATCAATGGCATCCCCACTGTGGTTGGGGTCTTCACCACACAGCTCAACAG
Seq A exon
GTGGGAACAAGCAGAACCCCGCCCCCCCACCAGGGGCTCCATGCTCCCTGTGGGAACTGGGCATGGCCCCCACTGTCAGCCTCGTCCTTATGATTGTATCACTTTTCAG
Seq C2 exon
CATTCCTGGTTCTGCAGTCTGTGCCTTTAGCATGGACGACATTGAGAAAGTGTTCAAAGGGCGGTTCAAAGAGCAGAAAACCCCAGACTCTGTTTGGACAGCAGTTCCCGAAGACAAAGTACCAAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200:ENSMUST00000103241:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.111
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(16.9=100)
A:
NA
C2:
PF0140314=Sema=FE(10.4=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:
CCTTAAGGCTCGGCTGAACTG
R:
TTCGGGAACTGCTGTCCAAAC
Band lengths:
247-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types