MmuINT0141245 @ mm9
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56266901-56267890:-
Coord C1 exon
chr17:56267673-56267890
Coord A exon
chr17:56267033-56267672
Coord C2 exon
chr17:56266901-56267032
Length
640 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
CTGCCTCACCCCCTCCGCAGCAT
3' ss Score
9.8
Exon sequences
Seq C1 exon
GTGGTGGTGTCTCGAGTGGCCCGTGTGTGCAAGAATGACGTGGGCGGCTCGCCACGAGTGCTGGAGAAGCAGTGGACTTCCTTCCTGAAGGCCCGGCTCAACTGCTCAGTGCCAGGGGATTCACACTTCTACTTCAACGTCCTGCAGGCTGTGACGGGCGTGGTGAGCCTGGGTGGTCGTCCGGTGATCCTCGCTGTCTTCTCAACTCCTAGCAACAG
Seq A exon
GTCAGCCCTTGCCATCAGGGGCCCACTGCGGGTGTTTGTTGGCCAGAATCCCAGTGTTCACACACTAGTCGGCAAATATTCTTTGCTGTCCTGTGTTGGGCAGCATTGGTCCCAGGAGACCTCTATGCCAATCTGGGGCCAAAGAATGAAAGAAACACTGGAGTCCTCTCACCCTACAGGACATGGCAGGAAAGGCTCCTGAAGGAGGGACATTGGGGTGTGGAAGGGGGAATAGTACATGAGAAGGGTCCAAGACTGTGCTAGTCAGAGGAAGGAGGCCTATGTGGCTGGTGTGGAGGGAGACAATGTGATCAAGGAATGTGTTAGAATTATGGAAGATTGCACAGTGGCACAGGGCCTAGACTTGGGTCTGAGAGCATGAGGGAGCCATGGACAAATGGGGATCAGCAAGCATGGCCTCTGGGCACTAAATATTCAGGAACTTACTAAATACTCAGTGAGAACTGAGAACGTGCAAAGACCCAGGGCAGAGGTCTAGGGAAGCCAGTCGCACAGTGGTCCAACCTGGGGATGTTCTGGAGGTGGAGTGGCTTGTGTTGCTCAGATGAGAGAAAGAGCAGGGAGACCCAGAGATGGTGCCACCCCCACCCAGCTCAGCACTGCCTCACCCCCTCCGCAG
Seq C2 exon
CATCCCCGGCTCAGCCGTCTGCGCCTTTGACATGAACCAAGTGGCTGCTGTGTTTGAAGGCCGCTTCCGGGAACAGAAGTCGCCTGAGTCGATCTGGACACCAGTGCCTGAAGACCAAGTGCCACGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227-Sema6b:NM_001130456:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.289
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.1=100)
A:
NA
C2:
PF0140314=Sema=FE(10.5=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:
TGGTGGTGTCTCGAGTGGC
R:
CGTGGCACTTGGTCTTCAGG
Band lengths:
343-983
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: