MmuINT0141246 @ mm10
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56126940-56127609:-
Coord C1 exon
chr17:56127478-56127609
Coord A exon
chr17:56127090-56127477
Coord C2 exon
chr17:56126940-56127089
Length
388 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACA
5' ss Score
5.49
3' ss Seq
TGCTCCTCATCTTCCCCCAGGCC
3' ss Score
10.32
Exon sequences
Seq C1 exon
CATCCCCGGCTCAGCCGTCTGCGCCTTTGACATGAACCAAGTGGCTGCTGTGTTTGAAGGCCGCTTCCGGGAACAGAAGTCGCCTGAGTCGATCTGGACACCAGTGCCTGAAGACCAAGTGCCACGGCCCAG
Seq A exon
GTGACAGTGACTTCTGTCTTTACAGGGTCCTTACAGTAGCTGGTTTGGGGGAGGTCAGCTCAGTGTCGGGTCAGGAGACAATGGAGGGACACAAGTTTGTGAAGGAAGACACGAGGAAGCCATCATGAAGGGCCAGGCAGTCAATGCTCTTCATTTGTTGAGGGCAGAGGGCAAGTGTGGGCAAAGACCCTGGAGTAGAGGGCATGGCCTGTGTGAGGCCCAGGCAAATCAGATCAGAAAGTACAGAGGTCCCGAGGCTACAGTGAGTCAGATCATGGAAACCCTAAGAGTGGGGAGCCATTCAAACCGGGTCCCAAGATGCCCCAGAGAATCAGGGCCTCATTGTGGGGTCCTGGCATCCTCCCTGATGCTCCTCATCTTCCCCCAG
Seq C2 exon
GCCTGGGTGCTGCGCGGCACCTGGCATGCAGTACAACGCGTCCAGTGCCCTCCCTGACGAGATCCTCAACTTTGTAAAGACCCACCCACTGATGGATGAGGCAGTACCTTCCCTGGGTCACTCGCCGTGGATTGTGAGAACTCTGATGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227:ENSMUST00000001256:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.289 A=NA C2=0.059
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.5=100)
A:
NA
C2:
PF0140314=Sema=FE(11.9=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:
CGTCTGCGCCTTTGACATGAA
R:
CAGAGTTCTCACAATCCACGGC
Band lengths:
262-650
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