MmuINT0141252 @ mm9
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56271921-56272291:-
Coord C1 exon
chr17:56272139-56272291
Coord A exon
chr17:56272045-56272138
Coord C2 exon
chr17:56271921-56272044
Length
94 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
CCTTCCACTCCCTCCCTTAGACT
3' ss Score
9.1
Exon sequences
Seq C1 exon
GTGTCATCTGTGGTCATCCGGTCCTCACCATGTGGACCCCGCGAGTGCCCCCTCCACGCCCGGCCCTGTCGTTTTTCCTGCTGTTGCTCCTGGGGGTCACCTATGGCCTTTTCCCAGAAGAACCACCTCCACTCAGCGTGGCTCCCAGGGACT
Seq A exon
GTGAGTCTGGGGAGAGATGGGCAGGGGTGTGTCAGGGTCTCTGGTACACAGGATCTTGTTTCCAAATGAACCCTCCTTCCACTCCCTCCCTTAG
Seq C2 exon
ACTTGAGCCACTATCCCGTGTTCGTGGGCAGCGGGCCTGGTCGTCTGACCGCTGCGGAGGGTGCTGAGGACCTCAACATCCAGAGAGTGCTACGTGTTAACAGGACACTGTTCATTGGGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227-Sema6b:NM_001130456:2
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=0.048 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(4.0=40.5)
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:
TGTCATCTGTGGTCATCCGGT
R:
ACACGGGATAGTGGCTCAAGT
Band lengths:
173-267
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: