MmuINT0141286 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124479317-124479994:+
Coord C1 exon
chr2:124479317-124479479
Coord A exon
chr2:124479480-124479882
Coord C2 exon
chr2:124479883-124479994
Length
403 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TAGCCCATTTTTACTTGCAGATT
3' ss Score
7.48
Exon sequences
Seq C1 exon
GTAGCTAAGTGGGACTTCTGAGGAGGGGGAGCTCAGATTTCTTCTTGGCCAACCATGGGGTTCCTTCTGCTTTGGTTCTGCGTGCTGTTCCTTCTGGTCTCCAGGTTACGGGCGGTCAGCTTCCCAGAAGACGATGAGCCCCTCAACACGGTTGACTATCACT
Seq A exon
GTAAGTCACACAAAGCCATTTCCTCGTTTGCAACGGAAGCCTTTTGTTTGTCTTTGCCTAGGTCTATTCATTTTCAGCATCAGAGACAAATTTTAATATGTCTTTACAATGTTTTGCACATTAAATCATCTGCAGTCTTTCCCTCGGCTGTGCAGAAACTGAGCCAGTTCTGTTGGGCGCCATCCTGCAGCAGCCCAGACATAGAGATTATATATTTTCAGTAAAAAAGAAAAAGACCATTTGCTGACAATTCTCCATCTTTTACTAATTTATATTCAAGACCTTAAGAGAGGAATTTAGTTAAAACCCTTCCTACAAGTGCTATATACAGCTAATCAATGCTGGCTATTGATTCTTCAGCTCTGTAATCCTGACTGATGGTTTAGCCCATTTTTACTTGCAG
Seq C2 exon
ATTCAAGGCAATATCCGGTTTTTAGAGGACGCCCTTCAGGCAACGAATCGCAGCACAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199239:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(3.8=42.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTAAGTGGGACTTCTGAGGA
R:
GCCAGCAATATAAAGTGTGTCTCG
Band lengths:
271-674
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: