MmuINT0141284 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124485543-124486080:+
Coord C1 exon
chr2:124485543-124485620
Coord A exon
chr2:124485621-124485979
Coord C2 exon
chr2:124485980-124486080
Length
359 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
TGTCCCTTGTCCCTATGAAGGCT
3' ss Score
7.41
Exon sequences
Seq C1 exon
GTCTTGCATTGCATCACGTGACCCGTACTGTGGTTGGTTAAGCCAGGGAGTTTGTGAGAGAGTGACCCTAGGGATGCT
Seq A exon
GTAAGTACACTGGACCACCAAGCCATTTTCTCTCAGGGTAGCAACAGCTTAAAAACAAAATGCTTTAGCCCCAGCTCTACTGCTTTTCTTTTCCTTCATTTCTTGGTCTGGTGTGGGGGGGGGGGGGAGGGGGAGTTTTAAAAAAGATGATCTAAAATTTGAGAGGGGAATGAGATTTAGATACAACAAGCCTTGAGGGCAGTAGATTGTGAAGAGAGACAGTTTTGCTCTCTTAGGCACCCTTGTTAAACTAATTCCGTTGGCAAGCGTGTTGAATCGTTAGTGCACTCTCTCTGCTGACTCTCACTAACCAGTCTGTGTTCTCGGCTCTGTCCTGGTTGTCCCTTGTCCCTATGAAG
Seq C2 exon
GCTGTTAACCGAAGACTTCTTTGCTTTCCATAACCACAGCCCTGGAGGATATGAGCAGGACACGGAGTACGGCAACACAGCCCACCTAGGGGACTGCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199239:15
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.082
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(33.8=100)
A:
NA
C2:
PF0143720=PSI=FE(44.2=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: