MmuINT0141256 @ mm10
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56130706-56131214:-
Coord C1 exon
chr17:56131113-56131214
Coord A exon
chr17:56130797-56131112
Coord C2 exon
chr17:56130706-56130796
Length
316 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
AGATTCTGTCCTCCCTGCAGATG
3' ss Score
11.19
Exon sequences
Seq C1 exon
GGTGAGTGTCGGAACTTTGTCAAGGTGCTCCTGCTTCGCGATGAGTCCACGCTGTTCGTGTGCGGCTCCAATGCGTTCAATCCCATCTGCGCCAATTACAGT
Seq A exon
GTGAGTCTCAGCCCTTCCTTCCAAGACCCAGGGATCTACCTCACCCTCCATGTCCCCAGAGTCTCCTCCCAGCCATGCACATCCCTGTGCTAGGTTTGCCAGGCTTGTCCCACATCTCTTGCGGGACTGACGACAATAGACTTGGGCCCATTTCACAGACCATGAAACTGAGGTCCAGAAAGGTTAATTGCCTGGCCAGAATCACACAGCAATGCAATGTGAAGCTAGGGTTCTGGCTGGAGTGGCGGACTGGGGAACCCCGGAGCTGCCAGGCAGAGTGAGGAGATGTATTGCTTAGATTCTGTCCTCCCTGCAG
Seq C2 exon
ATGGACACACTGCAGCTTCTTGGTGACAGCATCAGCGGTATGGCCCGCTGCCCCTATGACCCCAAACATGCCAATGTCGCCCTCTTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227:ENSMUST00000001256:6
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(7.8=100)
A:
NA
C2:
PF0140314=Sema=FE(7.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAGTGTCGGAACTTTGTCA
R:
CTGAGAAGAGGGCGACATTGG
Band lengths:
193-509
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